fhcor: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor
Consider adding
  importFrom("stats", "cor")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘Omu_vignette.Rmd’
Found an obsolete/platform-specific call in the following function:
  ‘comp.freq’
Found the platform-specific device:
  ‘x11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
MLparameters: no visible global function definition for ‘optim’
comp.freq: no visible global function definition for ‘x11’
comp.freq: no visible global function definition for ‘par’
Undefined global functions or variables:
  optim par x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par")
  importFrom("stats", "optim")
to your NAMESPACE file.
generate.data: no visible global function definition for ‘rbinom’
least.common.ancestor: no visible global function definition for
  ‘na.omit’
oncotree.fit : estimate.error.rates: no visible global function
  definition for ‘optim’
plot.boottree: no visible global function definition for ‘par’
plot.boottree: no visible global function definition for
  ‘dev.interactive’
plot.boottree: no visible global function definition for ‘mtext’
plot.oncotree: no visible global function definition for ‘par’
plot.oncotree: no visible global function definition for ‘xinch’
plot.oncotree: no visible global function definition for ‘yinch’
plot.oncotree: no visible global function definition for ‘lines’
plot.oncotree: no visible global function definition for ‘rect’
plot.oncotree: no visible global function definition for ‘strwidth’
plot.oncotree: no visible global function definition for ‘strheight’
plot.oncotree: no visible global function definition for ‘text’
Undefined global functions or variables:
  dev.interactive lines mtext na.omit optim par rbinom rect strheight
  strwidth text xinch yinch
Consider adding
  importFrom("grDevices", "dev.interactive")
  importFrom("graphics", "lines", "mtext", "par", "rect", "strheight",
             "strwidth", "text", "xinch", "yinch")
  importFrom("stats", "na.omit", "optim", "rbinom")
to your NAMESPACE file.
ci.prop: no visible global function definition for ‘qf’
ci.prop: no visible global function definition for ‘qnorm’
ePCP: no visible global function definition for ‘qnorm’
sevennum: no visible global function definition for ‘na.omit’
sevennum: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  na.omit qf qnorm quantile
Consider adding
  importFrom("stats", "na.omit", "qf", "qnorm", "quantile")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘opencage.Rmd’
Running ‘testthat.R’ [26s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(OpenLand)
  > 
  > test_check("OpenLand")
  ── 1. Error: Behavior of summary_map (@test_generalfunctions.R#53)  ────────────
  Assigned data `c(as.numeric(names(value_map)[i]), value_map[[i]])` must be compatible with row subscript `i`.
  ✖ 1 row must be assigned.
  ✖ Assigned data has 2 rows.
  ℹ Only vectors of size 1 are recycled.
  Backtrace:
    1. testthat::expect_silent(...)
    9. OpenLand::summary_map(...)
   11. tibble:::`[<-.tbl_df`(`*tmp*`, i, c(1:2), value = c(1, 1983))
   12. tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   13. tibble:::vectbl_recycle_rhs(...)
   14. base::tryCatch(...)
   15. base:::tryCatchList(expr, classes, parentenv, handlers)
   16. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   17. value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 112 | SKIPPED: 0 | WARNINGS: 24 | FAILED: 1 ]
  1. Error: Behavior of summary_map (@test_generalfunctions.R#53) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘openNLPmodels.en’
Df2SpLinesDf: no visible global function definition for ‘slot’
PlotTraj: no visible global function definition for ‘par’
PlotTraj: no visible global function definition for ‘grid’
PlotTraj: no visible global function definition for ‘box’
PlotTrajFreq: no visible global function definition for ‘par’
PlotTrajFreq: no visible global function definition for ‘grid’
PlotTrajFreq: no visible global function definition for
  ‘colorRampPalette’
PlotTrajFreq: no visible global function definition for ‘legend’
PlotTrajFreq: no visible binding for global variable ‘title’
PlotTrajFreq: no visible global function definition for ‘dev.off’
ReadFiles: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  box colorRampPalette dev.off grid legend par read.table slot title
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off")
  importFrom("graphics", "box", "grid", "legend", "par", "title")
  importFrom("methods", "slot")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package suggested but not available for checking: ‘nbc4va’
nlsolve: no visible global function definition for ‘optim’
nlsolve: no visible global function definition for ‘runif’
optAUC: no visible global function definition for ‘var’
Undefined global functions or variables:
  optim runif var
Consider adding
  importFrom("stats", "optim", "runif", "var")
to your NAMESPACE file.
Found the following files/directories:
  ‘Graph_layout_Doptbd_trtE’
avg2Lower: no visible global function definition for ‘optimize’
classificationError.data.frame: no visible binding for global variable
  ‘na.omit’
classificationError.data.frame: no visible global function definition
  for ‘terms’
classificationError.data.frame: no visible binding for global variable
  ‘predict’
classpredict.lda: no visible global function definition for ‘predict’
simData: no visible global function definition for ‘rnorm’
simData: no visible global function definition for ‘runif’
simData: no visible global function definition for ‘var’
tnormAvg: no visible global function definition for ‘dnorm’
tnormAvg: no visible global function definition for ‘pnorm’
yapprox: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dnorm na.omit optimize pnorm predict rnorm runif terms var
Consider adding
  importFrom("stats", "approx", "dnorm", "na.omit", "optimize", "pnorm",
             "predict", "rnorm", "runif", "terms", "var")
to your NAMESPACE file.
print.optimbase: no visible global function definition for ‘str’
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘UserGuide.Rmd’
Found the following files/directories:
  ‘Graph_layout_Doptrcd_trtE’
getMinimumArborescence: no visible global function definition for
  ‘capture.output’
getMinimumCutTree: no visible global function definition for
  ‘capture.output’
getMinimumCutTree: no visible global function definition for ‘par’
getMinimumSpanningTree: no visible global function definition for
  ‘capture.output’
getShortestPathTree: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output par
Consider adding
  importFrom("graphics", "par")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Agrestiind.CI: no visible global function definition for ‘qnorm’
BPexact.CI: no visible global function definition for ‘uniroot’
BPmidp.CI: no visible global function definition for ‘uniroot’
Cornfieldexact.CI: no visible global function definition for ‘uniroot’
Cornfieldmidp.CI: no visible global function definition for ‘uniroot’
Gart.CI: no visible global function definition for ‘qnorm’
Invsinh.CI: no visible global function definition for ‘qnorm’
Woolf.CI: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm uniroot
Consider adding
  importFrom("stats", "qnorm", "uniroot")
to your NAMESPACE file.
BTLboost: no visible global function definition for ‘as.formula’
design: no visible global function definition for ‘as.formula’
wide2long: no visible global function definition for ‘reshape’
Undefined global functions or variables:
  as.formula reshape
Consider adding
  importFrom("stats", "as.formula", "reshape")
to your NAMESPACE file.
'library' or 'require' call to ‘psych’ which was already attached by Depends.
  Please remove these calls from your code.
Found the following files/directories:
  ‘orddom_csv.txt’ ‘orddom_csv_tab.txt’ ‘tmp_r.txt’
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.
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 ‘lines’
predict.ordPen: no visible global function definition for ‘plogis’
Undefined global functions or variables:
  anova devAskNewPage grey lines lm plogis sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "grey")
  importFrom("graphics", "lines")
  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 ‘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 ‘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 points postscript sd write.table
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "postscript")
  importFrom("graphics", "par", "points")
  importFrom("stats", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘cluster of fitted mean data.eps’ ‘cluster of fitted mean data.txt’
  ‘cluster of raw data.txt’
boat3d: no visible global function definition for ‘rgl.cur’
boat3d: no visible global function definition for ‘open3d’
boat3d: no visible global function definition for ‘clear3d’
boat3d: no visible global function definition for ‘bg3d’
boat3d: no visible global function definition for ‘rgl.set’
boat3d: no visible global function definition for ‘triangles3d’
boat3d: no visible global function definition for ‘quads3d’
boat3d: no visible global function definition for ‘decorate3d’
boat3d: no visible global function definition for ‘scatterplot3d’
orientlm: no visible global function definition for ‘model.matrix’
orientlm: no visible global function definition for ‘lm’
Undefined global functions or variables:
  bg3d clear3d decorate3d lm model.matrix open3d quads3d rgl.cur
  rgl.set scatterplot3d triangles3d
Consider adding
  importFrom("stats", "lm", "model.matrix")
to your NAMESPACE file.
File ‘OriGen/libs/OriGen.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_rewind’, possibly from ‘rewind’ (Fortran)
    Object: ‘OriGen.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
mdr.c: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘dcemriS4’
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_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
  points
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "points")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘OTclust.Rmd’
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.
Found the following files/directories:
  ‘result.txt’
loadCSVtoP2distance: no visible global function definition for
  ‘read.table’
p2distance : calcularDistancia: no visible binding for global variable
  ‘sd’
p2distance : ordenarVariables: no visible global function definition
  for ‘cor’
p2distance : calculoFactoresPonderacion: no visible global function
  definition for ‘lm’
p2distance: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor lm read.table sd
Consider adding
  importFrom("stats", "cor", "lm", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' call to ‘survival’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
p3state: no visible global function definition for ‘survfit’
p3state: no visible global function definition for ‘terms’
p3state: no visible global function definition for ‘as.formula’
p3state: no visible global function definition for ‘coxph’
p3state: no visible binding for global variable ‘na.exclude’
plot.p3state: no visible global function definition for ‘matplot’
plot.p3state: no visible global function definition for ‘devAskNewPage’
plot.p3state: no visible global function definition for ‘persp’
plot.p3state: no visible global function definition for ‘colours’
plot.p3state: no visible global function definition for
  ‘filled.contour’
Undefined global functions or variables:
  as.formula colours coxph devAskNewPage filled.contour matplot
  na.exclude persp survfit terms
Consider adding
  importFrom("grDevices", "colours", "devAskNewPage")
  importFrom("graphics", "filled.contour", "matplot", "persp")
  importFrom("stats", "as.formula", "na.exclude", "terms")
to your NAMESPACE file.
pacbpred : thetaFunc: no visible global function definition for ‘lsfit’
pacbpred : thetaFunc: no visible global function definition for ‘rnorm’
pacbpred: no visible global function definition for ‘var’
pacbpred: no visible global function definition for ‘runif’
pacbpred: no visible global function definition for ‘rnorm’
pacbpred: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  lsfit rbinom rnorm runif var
Consider adding
  importFrom("stats", "lsfit", "rbinom", "rnorm", "runif", "var")
to your NAMESPACE file.
Missing or unexported objects:
  ‘devtools::use_build_ignore’ ‘devtools::use_travis’
Non-standard files/directories found at top level:
  ‘DESCRIPTION_EX’ ‘divers’ ‘main.R’ ‘testsDev’
[,ClassW: warning in switch(EXP = i, u1 = {: partial argument match of
  ‘EXP’ to ‘EXPR’
[,ClassW: warning in return(x@u1): partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in }, u2 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in return(x@u2): partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in }, w1 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in return(x@w1): partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in }): partial argument match of ‘EXP’ to ‘EXPR’
[<-,ClassW: warning in switch(EXP = i, u1 = {: partial argument match
  of ‘EXP’ to ‘EXPR’
[<-,ClassW: warning in x@u1 <- value: partial argument match of ‘EXP’
  to ‘EXPR’
[<-,ClassW: warning in }, u2 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[<-,ClassW: warning in x@u2 <- value: partial argument match of ‘EXP’
  to ‘EXPR’
[<-,ClassW: warning in }, w1 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[<-,ClassW: warning in x@w1 <- value: partial argument match of ‘EXP’
  to ‘EXPR’
[<-,ClassW: warning in }): partial argument match of ‘EXP’ to ‘EXPR’
paf: no visible global function definition for ‘as.formula’
paf: no visible global function definition for ‘model.response’
paf: no visible global function definition for ‘model.frame’
paf: no visible global function definition for ‘model.matrix’
plot.paf: no visible global function definition for ‘lines’
Undefined global functions or variables:
  as.formula lines model.frame model.matrix model.response
Consider adding
  importFrom("graphics", "lines")
  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.
Found the following files/directories:
  ‘GDPgrowthRESULTS.csv’
Package which this enhances but not available for checking: ‘CorShrink’
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘lattice’ ‘vegan’
  Please remove these calls from your code.
Found the following files/directories:
  ‘Dispersion.pdf’
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’
SignificantSubcluster: no visible global function definition for
  ‘order.dendrogram’
SignificantSubcluster: no visible global function definition for
  ‘fisher.test’
Undefined global functions or variables:
  as.dendrogram as.hclust ecdf fisher.test is.leaf order.dendrogram
Consider adding
  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.
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.
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.
Found the following files/directories:
  ‘example.csv’ ‘example.tsv’ ‘example.xlsx’
.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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘introduction-to-parcoords-.Rmd’
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’
Undefined global functions or variables:
  coef ggm.test.edges predict sd var
Consider adding
  importFrom("stats", "coef", "predict", "sd", "var")
to your NAMESPACE file.
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.
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.
Found the following files/directories:
  ‘co2’ ‘co2.1’ ‘co2.2’ ‘co2s.1’ ‘co2s.2’ ‘ctm.1’ ‘ctm.2’ ‘m’ ‘m.1’
  ‘m.2’ ‘test’ ‘test.1’ ‘test.2’ ‘testa.1’ ‘testa.2’ ‘xfile.1’
  ‘xfile.2’
Warning: no function found corresponding to methods exports from ‘partsm’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
parviol: no visible global function definition for ‘plot.new’
parviol: no visible global function definition for ‘plot.window’
parviol: no visible global function definition for ‘title’
parviol: no visible global function definition for ‘lines’
parviol: no visible global function definition for ‘text’
parviol: no visible global function definition for ‘rgb’
selecto: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot.new plot.window rgb text title
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "plot.new", "plot.window", "text",
             "title")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘ape’ ‘caper’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
conch: no visible global function definition for ‘read.tree’
conch: no visible global function definition for ‘reorder’
conch: no visible global function definition for ‘read.nexus’
conch: no visible global function definition for ‘.compressTipLabel’
conch: no visible global function definition for ‘drop.tip’
conch: no visible global function definition for ‘extract.clade’
conch: no visible global function definition for ‘which.edge’
conch: no visible global function definition for ‘write.tree’
pastis_main: no visible global function definition for ‘combn’
read_input: no visible global function definition for ‘read.tree’
read_input: no visible global function definition for ‘reorder’
read_input: no visible global function definition for ‘read.csv’
read_input: no visible global function definition for ‘read.dna’
Undefined global functions or variables:
  .compressTipLabel combn drop.tip extract.clade read.csv read.dna
  read.nexus read.tree reorder which.edge write.tree
Consider adding
  importFrom("stats", "reorder")
  importFrom("utils", "combn", "read.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘pastis_data_1’ ‘pastis_data_2’ ‘pastis_data_3’
'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.
Found the following files/directories:
  ‘Minimal-concordance.tex’ ‘Minimal.Rnw’ ‘Minimal.pdf’
  ‘Minimal.synctex.gz’ ‘Minimal.tex’ ‘figure’
Package vignette with placeholder title ‘Vignette Title’:
  ‘pathlibr.Rmd’
Packages in Depends field not imported from:
  ‘plspm’ ‘tester’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
add_noise: no visible global function definition for ‘rnorm’
estimate_risk_dream6 : <anonymous>: no visible global function
  definition for ‘var’
generate_sample: no visible global function definition for ‘rnorm’
generate_sample: no visible global function definition for ‘runif’
sample_function: no visible global function definition for ‘runif’
sample_function : <anonymous>: no visible global function definition
  for ‘var’
sample_function_multi_mod_weight: no visible global function definition
  for ‘runif’
sample_function_multi_mod_weight : <anonymous>: no visible global
  function definition for ‘var’
sample_function_single_mod: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  rnorm runif var
Consider adding
  importFrom("stats", "rnorm", "runif", "var")
to your NAMESPACE file.
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.
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.
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 points prcomp quantile symbols
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "grid", "legend", "points", "symbols")
  importFrom("stats", "cor", "prcomp", "quantile")
to your NAMESPACE file.
PCDReg.wf: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
Found the following files/directories:
  ‘AbsolutePlot_Absolute Risk.pdf’ ‘ContrastPlot_OR.pdf’
Package suggested but not available for checking: ‘FFTrees’
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.
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').
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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘peakPick-vignette.Rmd’
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 ‘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 ‘identify’
peplot: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  boxplot cycle identify is.ts lag mtext par pchisq segments title ts
  ts.intersect
Consider adding
  importFrom("graphics", "boxplot", "identify", "mtext", "par",
             "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 ‘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 rnorm title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "axis", "lines", "par", "title")
  importFrom("stats", "rnorm")
to your NAMESPACE file.
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').
Found the following files/directories:
  ‘A.txt’ ‘Ainv.txt’
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.
'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.
complexity.LASSO: no visible global function definition for ‘profL1’
complexity.ipec.CoxBoost: no visible global function definition for
  ‘CoxBoost’
complexity.ipec.CoxBoost: no visible global function definition for
  ‘locfit’
complexity.mincv.CoxBoost: no visible global function definition for
  ‘cv.CoxBoost’
complexity.ripec.CoxBoost: no visible global function definition for
  ‘CoxBoost’
complexity.ripec.CoxBoost: no visible global function definition for
  ‘locfit’
extract: no visible global function definition for ‘findGlobals’
fit.CoxBoost: no visible global function definition for ‘CoxBoost’
fit.LASSO: no visible global function definition for ‘penalized’
Undefined global functions or variables:
  CoxBoost cv.CoxBoost findGlobals locfit penalized profL1
Found the following files/directories:
  ‘PARMA21del1_ident’
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').
Found the following files/directories:
  ‘permus_per_dist_4’ ‘permus_per_shape_bin_4_0’
  ‘permus_per_shape_bin_4_1’ ‘permus_per_shape_bin_4_2’
  ‘permus_per_shape_bin_4_3’
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.
Found the following files/directories:
  ‘neural_network-s0000r1000.html’ ‘neural_network-s1000r1000.html’
  ‘neural_network-s2000r1000.html’ ‘neural_network-s3000r1000.html’
Found the following files/directories:
  ‘Myfile.txt’
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.
Found the following files/directories:
  ‘animation.gif’
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.
Found the following files/directories:
  ‘test.pdf’
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’
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’
nahu: no visible global function definition for ‘interaction.plot’
nahu: no visible global function definition for ‘reorder’
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’
Undefined global functions or variables:
  cor interaction.plot median reorder sd var
Consider adding
  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').
Found the following files/directories:
  ‘1khz.wav’ ‘snd.wav’
Package vignette with placeholder title ‘Vignette Title’:
  ‘photosynthesis-introduction.Rmd’
Package suggested but not available for checking: ‘OutbreakTools’
Found the following files/directories:
  ‘output_values’
Unknown packages ‘surface’, ‘bayou’ in Rd xrefs
Found the following files/directories:
  ‘subj_slp_sum.csv’ ‘wa_ps_V811043_sum.csv’
incident: no visible global function definition for ‘splinefun’
incident: no visible global function definition for ‘integrate’
phytoprod: no visible global function definition for ‘approx’
phytoprod: no visible global function definition for ‘splinefun’
phytoprod: no visible global function definition for ‘integrate’
reflectance: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx integrate splinefun
Consider adding
  importFrom("stats", "approx", "integrate", "splinefun")
to your NAMESPACE file.
File which contains pragma(s) suppressing diagnostics:
  ‘src/pijavski.cpp’
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’
Running ‘test-async.R’ [14s/25s]
  Running ‘testthat.R’ [3s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pkgcache)
  > 
  > test_check("pkgcache")
  ── 1. Error: load_primary_pkgs (@test-metadata-cache.R#191)  ───────────────────
  No metadata available
  Backtrace:
   1. pkgcache:::synchronise(get_private(cmc)$load_primary_pkgs(oneday()))
   2. get_private(cmc)$load_primary_pkgs(oneday())
   3. pkgcache:::cmc__load_primary_pkgs(self, private, max_age)
   4. private$update_replica_rds(alert = FALSE)
   5. pkgcache:::cmc__update_replica_rds(self, private, alert)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 305 | SKIPPED: 28 | WARNINGS: 2 | FAILED: 1 ]
  1. Error: load_primary_pkgs (@test-metadata-cache.R#191) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Found the following files/directories:
  ‘Indometh_Bolus_Linear_CoreOutput.txt’
  ‘Indometh_Bolus_Log_CoreOutput.txt’
  ‘Indometh_Infusion_Linear_CoreOutput.txt’
  ‘Indometh_Infusion_Log_CoreOutput.txt’ ‘Output’
  ‘Theoph_Linear_CoreOutput.txt’ ‘Theoph_Log_CoreOutput.txt’
Package suggested but not available for checking: ‘BradleyTerryScalable’
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.html’ ‘P2Run.png’
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:
  ‘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.
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 ‘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 quantile tail title var
  window
Consider adding
  importFrom("graphics", "axis", "box", "bxp", "lines", "matplot",
             "pairs", "par", "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.
print.densityEHpi: no visible global function definition for ‘str’
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
.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 ‘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 rexp rmultinom runif
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "kmeans", "mahalanobis", "optimize", "rexp",
             "rmultinom", "runif")
  importFrom("utils", "alarm")
to your NAMESPACE file.
dbm: no visible global function definition for ‘optim’
dbm: no visible global function definition for ‘new’
destat: no visible global function definition for ‘weighted.mean’
local.knn: no visible global function definition for ‘sd’
local.knn: no visible global function definition for ‘optim’
mdpref: no visible global function definition for ‘sd’
mdpref: no visible global function definition for ‘text’
mdpref: no visible global function definition for ‘lines’
phicom: no visible global function definition for ‘optim’
phicom: no visible global function definition for ‘new’
pl: no visible global function definition for ‘optim’
pl: no visible global function definition for ‘new’
rol: no visible global function definition for ‘nlm’
rol: no visible global function definition for ‘new’
wdbm: no visible global function definition for ‘optim’
wdbm: no visible global function definition for ‘new’
Undefined global functions or variables:
  lines new nlm optim sd text weighted.mean
Consider adding
  importFrom("graphics", "lines", "text")
  importFrom("methods", "new")
  importFrom("stats", "nlm", "optim", "sd", "weighted.mean")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'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.
smooth: no visible global function definition for ‘genoud’
Undefined global functions or variables:
  genoud
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.
Found the following significant warnings:
  Warning: `data_frame()` is deprecated as of tibble 1.1.0.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/poio.Rcheck/00install.out’ for details.
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.
Found the following files/directories:
  ‘pow.txt’
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.
Found the following files/directories:
  ‘Table.Output.html’
Package suggested but not available for checking: ‘pollimetrydata’
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.
Found the following files/directories:
  ‘polyfreqs-mcmc.out’
Package vignette with placeholder title ‘Vignette Title’:
  ‘polynomials.Rmd’
Found the following files/directories:
  ‘AbsorbedDrugMetabolites’ ‘CorrelationResults’
  ‘EndogenousMetabolites’ ‘HeatMap’ ‘PKresults’
  ‘SecondAbsorbedMetabolites’ ‘preprocessed-data’
Found the following files/directories:
  ‘SPAGfreqExample2.txt’ ‘SpagInputExample.txt’ ‘SpagOutExample.txt’
  ‘SpagTemp.txt’ ‘TetrasatExample.txt’ ‘atetraexample.txt’
  ‘atetratest.txt’ ‘exampleGMoutput.txt’ ‘forPOPDIST.txt’
  ‘genodiveExample.txt’ ‘readGMtest.txt’ ‘strtemp.txt’ ‘structtest.txt’
  ‘testGenoDive2.txt’ ‘testGenoDive3.txt’ ‘testPOPDIST.txt’
  ‘tetrasattest.txt’
Found the following files/directories:
  ‘test-data.R’ ‘test-inits.R’ ‘test.bug’ ‘test.cmd’
'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.
Found the following files/directories:
  ‘PopED_output_summary_D_cont_opt_1.txt’ ‘PopED_output_summary_RS.txt’
  ‘PopED_output_summary_mfea_opt_1.txt’ ‘test.csv’
Package suggested but not available for checking: ‘WhopGenome’
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.
Running ‘testthat.R’ [152s/235s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(portalr)
  > 
  > test_check("portalr")
  ── 1. Failure: default data path functions work if unset (@test-01-data-retrieva
  `m` does not match "Call `usethis::edit_r_environ\\(\\)` to open '.Renviron'".
  Actual value: ""
  
  ── 2. Failure: default data path functions work if unset (@test-01-data-retrieva
  `m` does not match "Store your data path with a line like:".
  Actual value: ""
  
  ── 3. Failure: default data path functions work if unset (@test-01-data-retrieva
  `m` does not match "PORTALR_DATA_PATH=".
  Actual value: ""
  
  ── 4. Failure: default data path functions work if unset (@test-01-data-retrieva
  `m` does not match "Make sure '.Renviron' ends with a newline!".
  Actual value: ""
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 194 | SKIPPED: 10 | WARNINGS: 4 | FAILED: 4 ]
  1. Failure: default data path functions work if unset (@test-01-data-retrieval.R#107) 
  2. Failure: default data path functions work if unset (@test-01-data-retrieval.R#108) 
  3. Failure: default data path functions work if unset (@test-01-data-retrieval.R#109) 
  4. Failure: default data path functions work if unset (@test-01-data-retrieval.R#110) 
  
  Error: testthat unit tests failed
  Execution halted
'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.
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
  ‘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’
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 pnorm points qnorm rexp rnorm uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "points")
  importFrom("stats", "dnorm", "optimize", "pnorm", "qnorm", "rexp",
             "rnorm", "uniroot")
to your NAMESPACE file.
Found the following files/directories:
  ‘Quad1.RData’ ‘Sp Env Data.RData’ ‘Sp PPM Data.RData’
  ‘SpEnvData.RData’ ‘Test.RData’ ‘TestPPM.RData’ ‘TestSP.RData’
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 ‘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 sd text var
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "hist", "pairs", "par", "text")
  importFrom("stats", "IQR", "median", "sd", "var")
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.
PKG_CXXFLAGS set in ‘src/Makevars.win’ without any corresponding files
gausspred: no visible global function definition for ‘qt’
mvapred: no visible global function definition for ‘qt’
Undefined global functions or variables:
  qt
Consider adding
  importFrom("stats", "qt")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘DESCRIPTION.bck’
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘predmixcor/R/firstlib.r’:
  .First.lib calls:
    cat("predmixcor loaded\n", "COPY RIGHT: Longhai Li\n", "http://math.usask.ca/~longhai\n",     "Type ?begin.predmixcor for help\n", sep = "")

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

Predict.mix: no visible global function definition for ‘dbinom’
abs_cor: no visible global function definition for ‘cor’
gen.alpha.IGamma: no visible global function definition for ‘qgamma’
gendata.mix: no visible global function definition for ‘runif’
gendata.mix: no visible global function definition for ‘rbeta’
mh1.unif: no visible global function definition for ‘runif’
train_predict_mix: no visible global function definition for ‘dbinom’
training: no visible global function definition for ‘runif’
training: no visible global function definition for ‘dbinom’
Undefined global functions or variables:
  cor dbinom qgamma rbeta runif
Consider adding
  importFrom("stats", "cor", "dbinom", "qgamma", "rbeta", "runif")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘COPYRIGHTS’
Copyright information should be in file inst/COPYRIGHTS
Found the following files/directories:
  ‘hista.png’ ‘plotcd.png’ ‘test.R’ ‘test.html’ ‘testR2html.R’
  ‘testglm.csv’ ‘testglm.html’ ‘testglm.tab’
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 ‘lines’
varperc: no visible global function definition for ‘text’
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 points screeplot strwidth terms text
Consider adding
  importFrom("graphics", "abline", "lines", "par", "points", "strwidth",
             "text")
  importFrom("stats", "model.matrix", "screeplot", "terms")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘priorcd.Rmd’
Found the following files/directories:
  ‘network.html’ ‘network_files’
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.mstep: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov dist
Consider adding
  importFrom("stats", "cov", "dist")
to your NAMESPACE file.
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’
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 poisson predict residuals rmultinom rnorm rt
  runif smooth.spline
Consider adding
  importFrom("stats", "dnorm", "dt", "dunif", "fitted", "poisson",
             "predict", "residuals", "rmultinom", "rnorm", "rt", "runif",
             "smooth.spline")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘MASS’ ‘nlme’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
Running ‘run-all.R’ [8s/20s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("ProjectTemplate")
  Loading required package: ProjectTemplate
  ── 1. Failure: Custom configuration is added to config (@test-add_config.R#12)  
  `load.project()` generated warnings:
  * 'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
  
  ✔ |  OK F W S | Context
  
  ⠏ |   0       | Example tests
  ✔ |   1       | Example tests
  
  ══ Results ═════════════════════════════════════════════════════════════════════
  OK:       1
  Failed:   0
  Warnings: 0
  Skipped:  0
  ✔ |  OK F W S | Context
  
  ⠏ |   0       | Example tests
  ✔ |   1       | Example tests
  
  ══ Results ═════════════════════════════════════════════════════════════════════
  OK:       1
  Failed:   0
  Warnings: 0
  Skipped:  0
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] TRUE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 852 | SKIPPED: 4 | WARNINGS: 281 | FAILED: 1 ]
  1. Failure: Custom configuration is added to config (@test-add_config.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
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 ‘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 predict quantile rbinom var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "binomial", "glm", "predict", "quantile", "rbinom",
             "var")
  importFrom("utils", "combn")
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.
'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 ‘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 points rgb2hsv
Consider adding
  importFrom("grDevices", "col2rgb", "hsv", "rgb2hsv")
  importFrom("graphics", "box", "contour", "lines", "par", "points")
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 suggested but not available for checking: ‘rdt’
Package vignette with placeholder title ‘Vignette Title’:
  ‘TargetDecoyFDR_Example.Rmd’
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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘PSF_vignette.Rmd’
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 files/directories:
  ‘gene_count_1.csv’
'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.
Non-standard file/directory found at top level:
  ‘orig’
Packages in Depends field not imported from:
  ‘EffectsRelBaseline’ ‘boot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
catEffectBootAdaptor: no visible binding for global variable ‘sumSqCat’
compExclusionFraction: no visible global function definition for
  ‘rpois’
compExclusionFraction: no visible global function definition for
  ‘t.test’
compExclusionFraction: no visible global function definition for ‘glm’
compExclusionFraction: no visible global function definition for
  ‘anova’
compPowerCatSelectivity: no visible binding for global variable
  ‘fRatioStat’
compPowerGeneralRespDetection: no visible binding for global variable
  ‘sumSqCat’
compPowerRespDetection: no visible binding for global variable
  ‘sumSqCat’
compRejectionFraction: no visible global function definition for
  ‘rpois’
compRejectionFraction: no visible global function definition for
  ‘t.test’
compRejectionFraction: no visible global function definition for ‘glm’
compRejectionFraction: no visible global function definition for
  ‘anova’
simCatResp: no visible global function definition for ‘rpois’
simNormCatResp: no visible global function definition for ‘rnorm’
testCatEffectBoot: no visible global function definition for ‘boot’
Undefined global functions or variables:
  anova boot fRatioStat glm rnorm rpois sumSqCat t.test
Consider adding
  importFrom("stats", "anova", "glm", "rnorm", "rpois", "t.test")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘multilevel’ ‘nlme’
A package should be listed in only one of these fields.
Non-standard file/directory found at top level:
  ‘README.txt’
'library' or 'require' calls to packages already attached by Depends:
  ‘multilevel’ ‘nlme’
  Please remove these calls from your code.
Package vignette with placeholder title ‘Vignette Title’:
  ‘ptstem.Rmd’
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 ‘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 quantile sd update
Consider adding
  importFrom("graphics", "lines")
  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.
.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').
Package vignette with placeholder title ‘Vignette Title’:
  ‘qaig-introduction.Rmd’
Found the following files/directories:
  ‘exampleplot_1_blockdist_1.png’ ‘exampleplot_1_blockdist_2.png’
  ‘exampleplot_1_blockdist_3.png’ ‘exampleplot_1_bootdist.png’
  ‘exampleplot_1_dist.png’ ‘exampleplot_1_histogramtest_EMD.png’
  ‘exampleplot_1_roc_dynamic.png’ ‘exampleplot_1_slidedist_1.png’
  ‘exampleplot_1_slidedist_2.png’ ‘exampleplot_1_slidedist_3.png’
  ‘exampleplot_1_trimmeddist.png’ ‘exampleplot_blockdist_1.png’
  ‘exampleplot_blockdist_2.png’ ‘exampleplot_blockdist_3.png’
  ‘exampleplot_bootdist.png’ ‘exampleplot_dist.png’
  ‘exampleplot_lim_dyn.png’ ‘exampleplot_lim_sig.png’
  ‘exampleplot_lim_sta.png’ ‘exampleplot_noc.png’
  ‘exampleplot_roc_dyn.png’ ‘exampleplot_roc_sta.png’
  ‘exampleplot_slidedist_1.png’ ‘exampleplot_slidedist_2.png’
  ‘exampleplot_slidedist_3.png’ ‘exampleplot_trimmeddist.png’
  ‘myworkflow_result.xml’ ‘test_2_roc_dynamic.png’ ‘test_4_dist.png’
  ‘test_5_blockdist_1.png’ ‘test_5_blockdist_2.png’
  ‘test_5_blockdist_3.png’ ‘test_6_slidedist_1.png’
  ‘test_6_slidedist_2.png’ ‘test_6_slidedist_3.png’
  ‘test_7_trimmeddist.png’ ‘test_8_bootdist.png’ ‘test_emd_1d.png’
  ‘test_emd_2d.png’ ‘test_jsd_1d.png’ ‘test_jsd_2d.png’
  ‘test_kld_1d.png’ ‘test_kld_2d.png’ ‘test_ms_1d.png’ ‘test_ms_2d.png’
  ‘test_rms_1d.png’ ‘test_rms_2d.png’
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 ‘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 points polygon
  printCoefmat
Consider adding
  importFrom("grDevices", "dev.cur", "dev.new")
  importFrom("graphics", "axis", "hist", "par", "points", "polygon")
  importFrom("stats", "density", "p.adjust", "printCoefmat")
to your NAMESPACE file.
Found the following files/directories:
  ‘EWAS_QC_graph_effectsize.png’ ‘EWAS_QC_graph_precision.png’
  ‘EWAS_QC_legend.txt’ ‘sample1.txt.gz’ ‘sample2.txt.gz’
  ‘sample_map.txt.gz’ ‘sample_output.graph_M.png’
  ‘sample_output.graph_QQ.png’ ‘sample_output.graph_p.png’
  ‘sample_output.graph_volcano.png’ ‘sample_output.histo.png’
  ‘sample_output.txt’ ‘sample_output1.graph_M.png’
  ‘sample_output1.graph_QQ.png’ ‘sample_output1.graph_p.png’
  ‘sample_output1.graph_volcano.png’ ‘sample_output1.histo.png’
  ‘sample_output2.graph_M.png’ ‘sample_output2.graph_QQ.png’
  ‘sample_output2.graph_p.png’ ‘sample_output2.graph_volcano.png’
  ‘sample_output2.histo.png’ ‘translation_table.txt’
Found the following files/directories:
  ‘sample_QQ.png’ ‘sample_QQ1.png’ ‘sample_QQ2.png’ ‘sample_QQ3.png’
  ‘sample_distribution.png’ ‘sample_graph_p-correlation.png’
  ‘sample_histogram.png’ ‘sample_histogram1.png’
  ‘sample_histogram2.png’ ‘sample_histogram3.png’
  ‘sample_plots_graph_M.png’ ‘sample_plots_graph_QQ.png’
  ‘sample_precision.png’ ‘sample_regional_association.png’
  ‘sample_skewness_kurtosis.png’
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 files/directories:
  ‘datInSFexample6_1pxCube.csv’ ‘datInSFexample6_1pxCubeA0.csv ’
  ‘datInSFexample6_1pxCubeA1.csv ’ ‘datInSFexample6_1pxCubeData.csv ’
  ‘datInSFexample6_1pxCubeVariable.csv’
  ‘datInSFexample6_1pxCubeVariableDomain.csv’
Found the following files/directories:
  ‘lambda.pdf’ ‘qqplot.pdf’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qtbase.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘qtl2’
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘qtlnet.Rnw’ using Sweave
Loading required package: qtl
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

Loading required package: sem
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:igraph’:

    normalize, path, union

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, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min


Attaching package: ‘graph’

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

    degree, edges, intersection

Loading required package: pcalg

Error: processing vignette 'qtlnet.Rnw' failed with diagnostics:
 chunk 2 
Error in igraph::graph.data.frame(edges, TRUE, vertices = vertices) : 
  Some vertex names in edge list are not listed in vertex data frame

--- failed re-building ‘qtlnet.Rnw’

SUMMARY: processing the following file failed:
  ‘qtlnet.Rnw’

Error: Vignette re-building failed.
Execution halted
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’
qualval: no visible global function definition for ‘qnorm’
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 pnorm qnorm rnorm sd tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("stats", "coef", "dbinom", "pchisq", "pnorm", "qnorm",
             "rnorm", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
Found the following calls to attach():
File ‘quantmod/R/attachSymbols.R’:
  attach(NULL, pos = pos, name = DB$name)
  attach(NULL, pos = pos, name = DB$name)
See section ‘Good practice’ in ‘?attach’.
Found the following files/directories:
  ‘Judge.pdf’
Found the following files/directories:
  ‘Example’
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.
Found the following files/directories:
  ‘chk1_1.dat’ ‘chk1_1.mem’ ‘chk1_1.noisy’
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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘R2DGC.Rmd’
'library' or 'require' call to ‘rgdal’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘matrixStats’ ‘rgdal’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following files/directories:
  ‘ndvi.rgf’
Found the following files/directories:
  ‘output.html’
Found the following calls to attach():
File ‘R2OpenBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
Found the following files/directories:
  ‘test.html’ ‘test.swf’
Found the following calls to attach():
File ‘R2WinBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
'library' or 'require' call to ‘rgl’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘lattice’ ‘leaps’ ‘rgl’ ‘s20x’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package vignette with placeholder title ‘Vignette Title’:
  ‘r511-intro.Rmd’
getsonde: no visible global function definition for ‘read.table’
plotsonde: no visible global function definition for ‘par’
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 ‘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 points polygon read.table sd segments
  text
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "par",
             "points", "polygon", "segments", "text")
  importFrom("stats", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘SondeFile.txt’
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.
Found the following files/directories:
  ‘blcs.dot’ ‘ex1.dot’ ‘ex1bridge1.dot’ ‘ex1bridge2.dot’
  ‘ex1bridge3.dot’ ‘ex1effect1.dot’ ‘ex1effect2.dot’ ‘gcmlinear.dot’
  ‘latent.dot’ ‘lcs.dot’ ‘mimic.dot’
.disableThreads: no visible global function definition for
  ‘stopCluster’
.enableThreads: no visible global function definition for ‘detectCores’
.enableThreads: no visible global function definition for
  ‘makePSOCKcluster’
.enableThreads: no visible global function definition for
  ‘clusterExport’
.enableThreads: no visible global function definition for ‘clusterCall’
.forwardSelection: no visible binding for global variable ‘var’
.forwardSelection: no visible global function definition for ‘glm’
.forwardSelection: no visible global function definition for ‘formula’
.forwardSelection: no visible global function definition for ‘binomial’
.forwardSelection: no visible global function definition for ‘lm’
.forwardSelection: no visible global function definition for ‘predict’
.predict.internal: no visible global function definition for ‘predict’
randomGLM: no visible binding for global variable ‘cor’
randomGLM: no visible binding for global variable ‘sd’
randomGLM: no visible global function definition for ‘var’
thinRandomGLM: no visible global function definition for ‘glm’
thinRandomGLM: no visible global function definition for ‘binomial’
thinRandomGLM: no visible global function definition for ‘lm’
Undefined global functions or variables:
  binomial clusterCall clusterExport cor detectCores formula glm lm
  makePSOCKcluster predict sd stopCluster var
Consider adding
  importFrom("stats", "binomial", "cor", "formula", "glm", "lm",
             "predict", "sd", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘randomGLM/R/randomGLM.R’:
  assign(".randomGLMparallelCluster", cluster, pos = ".GlobalEnv")
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.
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.
'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.
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.
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.
.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.
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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘RBitmoji.Rmd’
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rblpapi.Rcheck/00install.out’ for details.
SumTestSens: no visible global function definition for ‘pnorm’
binarysens: no visible global function definition for ‘dbinom’
hlsens: no visible global function definition for ‘wilcox.test’
iv_sens: no visible global function definition for ‘pnorm’
mcontrol: no visible global function definition for ‘pnorm’
psens: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dbinom pnorm wilcox.test
Consider adding
  importFrom("stats", "dbinom", "pnorm", "wilcox.test")
to your NAMESPACE file.
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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘rcane.Rmd’
Found the following files/directories:
  ‘rcanvec.cache’
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.
Found the following files/directories:
  ‘temp.RData’
.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.
Found the following files/directories:
  ‘data.csv’
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.
Found the following files/directories:
  ‘file1.arp’ ‘file2.arp’ ‘test.txt’ ‘test2.txt’
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.
Found the following files/directories:
  ‘outcmaesdisp.dat’
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.
managedata: no visible binding for global variable ‘data’
Undefined global functions or variables:
  data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
'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
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.
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’
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 ‘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 rect rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "image", "par", "rect", "text")
to your NAMESPACE file.
addLine: no visible global function definition for ‘abline’
ellipse: no visible global function definition for ‘approx’
ellipse: no visible global function definition for ‘tail’
Undefined global functions or variables:
  abline approx tail
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "approx")
  importFrom("utils", "tail")
to your NAMESPACE file.
Gauss: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘rcreds.Rmd’
Running ‘testthat.R’ [19s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("RCzechia")
  Loading required package: RCzechia
  Loading required package: sf
  Linking to GEOS 3.8.1, GDAL 3.0.4, PROJ 7.0.0
  ── 1. Error: (unknown) (@test-2-code.R#20)  ────────────────────────────────────
  'st_make_valid' is not an exported object from 'namespace:lwgeom'
  Backtrace:
    1. RCzechia::casti()
    9. RCzechia::union_sf(., "NAZ_OBEC")
    3. data[vec, ]
   10. lwgeom::st_make_valid(.)
   18. base::getExportedValue(pkg, name)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 145 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test-2-code.R#20) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Loading required package: sf
Linking to GEOS 3.8.1, GDAL 3.0.4, PROJ 7.0.0

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

RCzechia: downloading remote dataset.
RCzechia: downloading remote dataset.
udunits system database from /usr/share/xml/udunits
RCzechia: downloading remote dataset.
RCzechia: using temporary local dataset.
Quitting from lines 220-240 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
'st_make_valid' is not an exported object from 'namespace:lwgeom'
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
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 ‘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 rnorm runif segments terrain.colors title
  topo.colors
Consider adding
  importFrom("grDevices", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "filled.contour", "lines", "segments",
             "title")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
sumry_categorical: no visible global function definition for ‘freq’
sumry_continous: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  freq quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Found the following significant warnings:
  bits.c:1247:23: warning: array subscript 8 is outside array bounds of ‘unsigned int[1]’ [-Warray-bounds]
  bits.c:1265:18: warning: array subscript 9 is outside array bounds of ‘unsigned int[1]’ [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RDieHarder.Rcheck/00install.out’ for details.
mve_single_cvxr: no visible global function definition for ‘Semidef’
Undefined global functions or variables:
  Semidef
Error(s) in re-building vignettes:
  ...
--- re-building ‘Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd’ using rmarkdown
Loading required package: rJava
Loading required package: Rdroolsjars

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: 'purrr'

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

    set_names

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.thoughtworks.xstream.core.util.Fields (file:/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rdroolsjars/java/xstream-1.4.9.jar) to field java.util.TreeMap.comparator
WARNING: Please consider reporting this to the maintainers of com.thoughtworks.xstream.core.util.Fields
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
Quitting from lines 183-187 (Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd) 
Error: processing vignette 'Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd' failed with diagnostics:
Assigned data `paste(seq(as.numeric(lowerRange), as.numeric(upperRange)), collapse = ",")` must be compatible with existing data.
ℹ Error occurred for column `Indices`.
✖ No common type for `value` <character> and `x` <double>.
--- failed re-building ‘Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd’

SUMMARY: processing the following file failed:
  ‘Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd’

Error: Vignette re-building failed.
Execution halted
'library' or 'require' call to ‘synchronicity’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following files/directories:
  ‘a.desc’ ‘b.desc’ ‘barrnumleft.desc’ ‘barrsense.desc’ ‘c.desc’
  ‘m.desc’ ‘u.desc’ ‘x’ ‘x.desc’
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.
Found the following files/directories:
  ‘example.pdf’
Found the following files/directories:
  ‘temp.txt’ ‘temp2.csv’ ‘temp3.rda’
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(readroper)
  readroper package loaded.
  > 
  > test_check("readroper")
  ── 1. Error: First row of multicard dataset matches (@test-readroper.R#4)  ─────
  Must subset rows with a valid subscript vector.
  ℹ Logical subscripts must match the size of the indexed input.
  ✖ The input has size 1976 but the subscript `card_v` has size 2.
  Backtrace:
    1. readroper::read_rpr(...)
   16. vctrs:::stop_indicator_size(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: First row of multicard dataset matches (@test-readroper.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Non-standard file/directory found at top level:
  ‘devel’
'library' or 'require' calls to packages already attached by Depends:
  ‘leaps’ ‘mgcv’
  Please remove these calls from your code.
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of ‘env’ to ‘envir’
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of ‘env’ to ‘envir’
bestmods: no visible global function definition for ‘abline’
bestmods: no visible global function definition for ‘axis’
bestmods: no visible global function definition for ‘lines’
cic: no visible global function definition for ‘lsfit’
cic: no visible global function definition for ‘var’
cvic: no visible global function definition for ‘lsfit’
cvic: no visible global function definition for ‘lm’
eic: no visible global function definition for ‘lsfit’
eic: no visible global function definition for ‘lm’
ic.min: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘var’
xy: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘reams/R/xy.R’:
  assign(xname, X, env = .GlobalEnv)
  assign(yname, y, env = .GlobalEnv)
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.
Running ‘test-all.R’ [4s/9s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > # Modeled after the R6 testing structure: https://github.com/wch/R6/blob/master/tests/testthat.R
  > library(testthat)
  > library(REDCapR)
  > 
  > testthat::test_check("REDCapR")
  ── 1. Failure: validate_no_logical -concern dataset (@test-validate.R#36)  ─────
  ds$field_index not equal to 2.
  names for target but not for current
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 135 | SKIPPED: 79 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: validate_no_logical -concern dataset (@test-validate.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following files/directories:
  ‘Filled.RData’ ‘cleaned.RData’ ‘days’ ‘gridded’
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’
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 predict residuals terms
Consider adding
  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.
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.
Found the following files/directories:
  ‘EnvironmentalA.txt’ ‘EnvironmentalB.txt’ ‘Example.txt’
  ‘Example_Predictions.txt’ ‘Example_RRDist.txt’
  ‘Example_RRDistCol.TIF’ ‘Example_RRDistGrey.TIF’ ‘GeneticA.txt’
  ‘GeneticB.txt’ ‘Inds.txt’
Non-standard files/directories found at top level:
  ‘prebuild.sh’ ‘regtest-Ex.R’
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.
'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
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.
duane: no visible global function definition for ‘optim’
duane.plot: no visible global function definition for ‘lines’
duane.plot: no visible global function definition for ‘legend’
duane.plot: no visible global function definition for ‘title’
littlewood.verall: no visible global function definition for ‘optim’
littlewood.verall.plot: no visible global function definition for
  ‘lines’
littlewood.verall.plot: no visible global function definition for
  ‘legend’
littlewood.verall.plot: no visible global function definition for
  ‘title’
moranda.geometric: no visible global function definition for ‘optimize’
moranda.geometric.plot: no visible global function definition for
  ‘lines’
moranda.geometric.plot: no visible global function definition for
  ‘legend’
moranda.geometric.plot: no visible global function definition for
  ‘title’
musa.okumoto: no visible global function definition for ‘optimize’
musa.okumoto.plot: no visible global function definition for ‘lines’
musa.okumoto.plot: no visible global function definition for ‘legend’
musa.okumoto.plot: no visible global function definition for ‘title’
rel.plot: no visible global function definition for ‘lines’
rel.plot: no visible global function definition for ‘segments’
rel.plot: no visible global function definition for ‘legend’
rel.plot: no visible global function definition for ‘title’
total.plot: no visible global function definition for ‘lines’
total.plot: no visible global function definition for ‘legend’
total.plot: no visible global function definition for ‘title’
Undefined global functions or variables:
  legend lines optim optimize segments title
Consider adding
  importFrom("graphics", "legend", "lines", "segments", "title")
  importFrom("stats", "optim", "optimize")
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 ‘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 ‘legend’
Undefined global functions or variables:
  abline coef legend lm par rnorm
Consider adding
  importFrom("graphics", "abline", "legend", "par")
  importFrom("stats", "coef", "lm", "rnorm")
to your NAMESPACE file.
Running examples in ‘rematch2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: re_exec
> ### Title: Extract Data From First Regular Expression Match Into a Data
> ###   Frame
> ### Aliases: re_exec $.rematch_records $.rematch_allrecords
> 
> ### ** Examples
> 
> name_rex <- paste0(
+   "(?<first>[[:upper:]][[:lower:]]+) ",
+   "(?<last>[[:upper:]][[:lower:]]+)"
+ )
> notables <- c(
+   "  Ben Franklin and Jefferson Davis",
+   "\tMillard Fillmore"
+ )
> # Match first occurrence
> pos <- re_exec(notables, name_rex)
> pos
Error: Input must be a vector, not a `rematch_records` object.
Backtrace:
     █
  1. ├─(function (x, ...) ...
  2. ├─tibble:::print.tbl(x)
  3. │ ├─cli::cat_line(format(x, ..., n = n, width = width, n_extra = n_extra))
  4. │ │ └─base::paste0(..., collapse = "\n")
  5. │ ├─base::format(x, ..., n = n, width = width, n_extra = n_extra)
  6. │ └─tibble:::format.tbl(x, ..., n = n, width = width, n_extra = n_extra)
  7. │   └─tibble::trunc_mat(x, n = n, width = width, n_extra = n_extra)
  8. │     ├─base::as.data.frame(head(x, n))
  9. │     ├─utils::head(x, n)
 10. │     └─utils:::head.data.frame(x, n)
 11. │       ├─base::do.call("[", args)
 12. │       ├─x[1:2, , drop = FALSE]
 13. │       └─tibble:::`[.tbl_df`(x, 1:2, , drop = FALSE)
 14. │         └─tibble:::tbl_subset_row(xo, i = i, i_arg)
 15. │           └─base::lapply(unclass(x), vec_slice, i = i)
 16. │             └─vctrs:::FUN(X[[i]
Execution halted
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’
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 rainbow runif write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf",
             "rainbow")
  importFrom("graphics", "image", "legend")
  importFrom("stats", "as.dendrogram", "dendrapply", "hclust", "heatmap",
             "is.leaf", "order.dendrogram", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘A.txt’ ‘minI.txt’ ‘minJ.txt’
GlobTestMissing: no visible global function definition for ‘lme’
GlobTestMissing: no visible global function definition for ‘anova’
TestStatSP: no visible global function definition for ‘pf’
TestStatSimple: no visible global function definition for ‘ginv’
TestStatSimple: no visible global function definition for ‘pf’
Undefined global functions or variables:
  anova ginv lme pf
Consider adding
  importFrom("stats", "anova", "pf")
to your NAMESPACE file.
Found the following files/directories:
  ‘PackageCites.bib’
delete: no visible global function definition for ‘menu’
doc_temp: no visible global function definition for ‘menu’
html5: no visible global function definition for ‘na.omit’
install_pandoc: no visible global function definition for
  ‘download.file’
new_report: no visible global function definition for ‘tail’
new_report: no visible global function definition for ‘head’
new_report: no visible global function definition for ‘menu’
presentation: no visible global function definition for ‘head’
presentation: no visible global function definition for ‘tail’
presentation: no visible global function definition for ‘menu’
repo2github: no visible global function definition for ‘download.file’
repo2github: no visible global function definition for ‘unzip’
reveal.js: no visible global function definition for ‘na.omit’
update_bib: no visible global function definition for ‘tail’
update_bib: no visible global function definition for ‘menu’
Undefined global functions or variables:
  download.file head menu na.omit tail unzip
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "download.file", "head", "menu", "tail", "unzip")
to your NAMESPACE file.
MBoxtest: no visible global function definition for ‘var’
jrparams: no visible global function definition for ‘prcomp’
jrparams: no visible global function definition for ‘predict’
jrparams: no visible global function definition for ‘qchisq’
jrparams: no visible global function definition for ‘qf’
Undefined global functions or variables:
  prcomp predict qchisq qf var
Consider adding
  importFrom("stats", "prcomp", "predict", "qchisq", "qf", "var")
to your NAMESPACE file.
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.
Found the following files/directories:
  ‘P.csv’ ‘correct_alpha.csv’ ‘correct_beta.csv’ ‘correct_gamma.csv’
  ‘correct_lambda.csv’ ‘correct_perm_list.csv’ ‘correct_psi.csv’
PKG_CFLAGS set in ‘src/Makevars’ without any corresponding files
Found the following files/directories:
  ‘forest.out’
.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').
Non-standard file/directory found at top level:
  ‘load.r’
Packages in Depends field not imported from:
  ‘gWidgets’ ‘gWidgetsRGtk2’ ‘plyr’ ‘reshape2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
reshapeGUI: no visible global function definition for ‘gwindow’
reshapeGUI: no visible global function definition for ‘gnotebook’
reshapeGUI: no visible global function definition for ‘size<-’
reshapeGUI: no visible global function definition for ‘ggroup’
reshapeGUI: no visible global function definition for ‘gtable’
reshapeGUI: no visible global function definition for ‘addSpring’
reshapeGUI: no visible global function definition for ‘gbutton’
reshapeGUI: no visible global function definition for ‘glabel’
reshapeGUI: no visible global function definition for ‘gedit’
reshapeGUI: no visible global function definition for ‘gcheckbox’
reshapeGUI: no visible global function definition for ‘gdf’
reshapeGUI: no visible global function definition for ‘visible<-’
reshapeGUI: no visible global function definition for
  ‘addHandlerClicked’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘gmessage’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘svalue’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘svalue<-’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘delete’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘add’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘gdf’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘visible<-’
reshapeGUI: no visible global function definition for
  ‘addHandlerChanged’
updateMeltCodeBox: no visible global function definition for ‘svalue<-’
Undefined global functions or variables:
  add addHandlerChanged addHandlerClicked addSpring delete gbutton
  gcheckbox gdf gedit ggroup glabel gmessage gnotebook gtable gwindow
  size<- svalue svalue<- visible<-
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').
plot.reweight: no visible global function definition for ‘par’
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 quantile rug
Consider adding
  importFrom("graphics", "par", "rug")
  importFrom("stats", "aggregate", "density", "quantile")
to your NAMESPACE file.
FDSNGetTimeSeries: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
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
Found the following files/directories:
  ‘Test.txt’
Error(s) in re-building vignettes:
  ...
--- re-building ‘RFmerge-RainfallExample-minimal.Rmd’ using rmarkdown

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Linking to GEOS 3.8.1, GDAL 3.0.4, PROJ 7.0.0
Loading required package: sp
rgdal: version: 1.4-8, (SVN revision 845)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 3.0.4, released 2020/01/28
 Path to GDAL shared files: 
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 7.0.0, March 1st, 2020, [PJ_VERSION: 700]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.4-1 
(C) 2019 M. Zambrano-Bigiarini and Oscar M. Baez-Villanueva (GPL >=3 license)
Type 'citation('RFmerge')' to see how to cite this package
Quitting from lines 268-274 (RFmerge-RainfallExample-minimal.Rmd) 
Error: processing vignette 'RFmerge-RainfallExample-minimal.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘RFmerge-RainfallExample-minimal.Rmd’

SUMMARY: processing the following file failed:
  ‘RFmerge-RainfallExample-minimal.Rmd’

Error: Vignette re-building failed.
Execution halted
.testLTS: no visible binding for global variable ‘stackloss’
Undefined global functions or variables:
  stackloss
Consider adding
  importFrom("datasets", "stackloss")
to your NAMESPACE file.
Found the following files/directories:
  ‘interactions.dot’
Package vignette with placeholder title ‘Vignette Title’:
  ‘rfVarImpOOB-vignette.Rmd’
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.
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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rgeolocate.Rcheck/00install.out’ for details.
Found the following significant warnings:
  /usr/include/gtk-2.0/gtk/gtktypeutils.h:236:1: warning: ‘GTypeDebugFlags’ is deprecated [-Wdeprecated-declarations]
  /usr/include/gtk-2.0/gtk/gtktooltips.h:73:3: warning: ‘GTimeVal’ is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rggobi.Rcheck/00install.out’ for details.
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
  Output from running autoreconf:
  aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
Found the following files/directories:
  ‘MD_display.csv’ ‘kola.c_COUNTRY_Cu.csv’
  ‘kola.c_COUNTRY_Cu_fences.txt’ ‘ogrady.mvalloc_mvalloc.csv’
  ‘sind.mat2open_NGR_summary.csv’ ‘sind.save_PC-loadings.csv’
  ‘sind.save_PC-scores.csv’ ‘test.save.mvalloc_mvalloc.csv’
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.
.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
Found the following files/directories:
  ‘mydata.rda’ ‘thedata.rda’
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 ‘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 points rainbow
Consider adding
  importFrom("grDevices", "gray", "rainbow")
  importFrom("graphics", "legend", "points")
  importFrom("stats", "approx")
to your NAMESPACE file.
plot.ijzip: no visible global function definition for ‘axis’
read.ijzip: no visible global function definition for ‘unzip’
Undefined global functions or variables:
  axis unzip
Consider adding
  importFrom("graphics", "axis")
  importFrom("utils", "unzip")
to your NAMESPACE file.
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.
Found the following files/directories:
  ‘mtcars.txt’
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 ‘testthat.R’ [3s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(riskclustr)
  > 
  > test_check("riskclustr")
  ── 1. Error: optimal_kmeans_d prints message if no seed is set (@test-optimal_km
  `i` must have one dimension, not 2.
  Backtrace:
    1. testthat::expect_message(...)
    6. riskclustr::optimal_kmeans_d(...)
    7. base::lapply(...)
    8. riskclustr:::FUN(X[[i]], ...)
    9. riskclustr::d(label = "cls", M = M, factors = factors, data = temp)
   12. tibble:::`[.tbl_df`(data, data[, label] == 0, )
   13. tibble:::tbl_subset_row(xo, i = i, i_arg)
   14. tibble:::vectbl_as_row_index(i, x, i_arg)
   15. tibble:::vectbl_as_row_location(i, nr, i_arg, assign)
   22. vctrs::vec_as_location(i, n, arg = as_label(i_arg))
  
  ── 2. Error: optimal_kmeans_d returns expected optimal_d value (@test-optimal_km
  `i` must have one dimension, not 2.
  Backtrace:
    1. testthat::expect_equal(...)
    4. riskclustr::optimal_kmeans_d(...)
    5. base::lapply(...)
    6. riskclustr:::FUN(X[[i]], ...)
    7. riskclustr::d(label = "cls", M = M, factors = factors, data = temp)
   10. tibble:::`[.tbl_df`(data, data[, label] == 0, )
   11. tibble:::tbl_subset_row(xo, i = i, i_arg)
   12. tibble:::vectbl_as_row_index(i, x, i_arg)
   13. tibble:::vectbl_as_row_location(i, nr, i_arg, assign)
   20. vctrs::vec_as_location(i, n, arg = as_label(i_arg))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 26 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 2 ]
  1. Error: optimal_kmeans_d prints message if no seed is set (@test-optimal_kmeans_d.R#49) 
  2. Error: optimal_kmeans_d returns expected optimal_d value (@test-optimal_kmeans_d.R#65) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘calculate_d.Rmd’ using rmarkdown
--- finished re-building ‘calculate_d.Rmd’

--- re-building ‘contribute.Rmd’ using rmarkdown
--- finished re-building ‘contribute.Rmd’

--- re-building ‘eh_test.Rmd’ using rmarkdown
--- finished re-building ‘eh_test.Rmd’

--- re-building ‘factor_pvalue.Rmd’ using rmarkdown

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

--- finished re-building ‘factor_pvalue.Rmd’

--- re-building ‘optimal_d.Rmd’ using rmarkdown
Quitting from lines 36-46 (optimal_d.Rmd) 
Error: processing vignette 'optimal_d.Rmd' failed with diagnostics:
`i` must have one dimension, not 2.
--- failed re-building ‘optimal_d.Rmd’

SUMMARY: processing the following file failed:
  ‘optimal_d.Rmd’

Error: Vignette re-building failed.
Execution halted
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 time
Consider adding
  importFrom("graphics", "abline", "lines")
  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.
Found the following files/directories:
  ‘B110711CD4.CSV’ ‘inputparam2.txt’ ‘itcout0.pdf’ ‘itcout1.eps’
  ‘origin_data.csv’
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.
Non-standard files/directories found at top level:
  ‘getsp.class’ ‘getsp.java’ ‘install-sh’ ‘jri’ ‘version’
Found the following possibly unsafe calls:
File ‘rJava/R/import.R’:
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File ‘rJava/R/jinit.R’:
  unlockBinding(x, .env)
  unlockBinding(x, pe)
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-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’

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.
Found the following files/directories:
  ‘Barplot’ ‘Boxplot’ ‘BubblePlot’ ‘CircularFV’ ‘DataTable’
  ‘Dendrogram’ ‘DensityPlot’ ‘Heatmap’ ‘HivePlot’ ‘Network’ ‘Piechart’
  ‘Scatter3d’ ‘ScatterPlot’ ‘Surface3d’ ‘SymHeatmap’ ‘WordCloud’
'library' or 'require' call to ‘rJava’ which was already attached by Depends.
  Please remove these calls from your code.
Package vignette with placeholder title ‘Vignette Title’:
  ‘rKIN_Introduction.Rmd’
cv.coef: no visible global function definition for ‘sd’
normalize.softmax: no visible global function definition for ‘plogis’
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 resid sd
Consider adding
  importFrom("graphics", "dotchart")
  importFrom("stats", "fitted", "influence", "plogis", "resid", "sd")
to your NAMESPACE file.
':::' 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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rlo.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘file.out’
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.
Running examples in ‘RmarineHeatWaves-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: detect
> ### Title: Detect heatwaves and cold-spells.
> ### Aliases: detect
> 
> ### ** Examples
> 
> ts_dat <- make_whole(sst_WA)
> res <- detect(ts_dat, climatology_start = "1983-01-01",
+               climatology_end = "2012-12-31")
Error: Assigned data `zoo::na.approx(tDat[59:61, no_NA], maxgap = 1, na.rm = TRUE)` must be compatible with existing data.
ℹ Error occurred for column `doy`.
✖ Can't cast <double[,31]> to <double>.
Can not decrease dimensions.
Backtrace:
    █
 1. └─RmarineHeatWaves::detect(...)
 2.   ├─base::`[<-`(...)
 3.   └─tibble:::`[<-.tbl_df`(...)
 4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 5.       └─tibble:::tbl_subassign_row(xj, i, value, value_arg)
 6.         └─base::tryCatch(...)
 7.           └─base:::tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)
Execution halted
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.
Found the following calls to attach():
File ‘Rmosek/R/builder.R’:
  attach(builderenv, pos, name, warn.conflicts)
See section ‘Good practice’ in ‘?attach’.
rms.pval: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘rmtl.Rmd’
dWishartSpike: no visible global function definition for ‘dnorm’
pWishartSpike: no visible global function definition for ‘pnorm’
qWishartSpike: no visible global function definition for ‘qnorm’
rWishartSpike: no visible global function definition for ‘qnorm’
rmp: no visible global function definition for ‘runif’
rtw: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dnorm pnorm qnorm runif
Consider adding
  importFrom("stats", "dnorm", "pnorm", "qnorm", "runif")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘DESeq’ ‘seqinr’ ‘topGO’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: ‘rnaturalearthhires’
well19937.validate: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
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.
RobRSVD: no visible global function definition for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
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’
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 ppois
  quantile s smooth.construct.cr.smooth.spec
  smooth.construct.ps.smooth.spec smooth.construct.tp.smooth.spec
Consider adding
  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.
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.
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’
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 predict rbinom rnorm sd
  terms
Consider adding
  importFrom("graphics", "abline", "lines")
  importFrom("stats", "as.formula", "model.frame", "predict", "rbinom",
             "rnorm", "sd", "terms")
  importFrom("utils", "methods")
to your NAMESPACE file.
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘data_mashups.Rmd’ using rmarkdown
Quitting from lines 43-45 (data_mashups.Rmd) 
Error: processing vignette 'data_mashups.Rmd' failed with diagnostics:
Timeout was reached: [api.opentreeoflife.org] Connection timed out after 10001 milliseconds
--- failed re-building ‘data_mashups.Rmd’

--- re-building ‘meta-analysis.Rmd’ using rmarkdown
Quitting from lines 107-109 (meta-analysis.Rmd) 
Error: processing vignette 'meta-analysis.Rmd' failed with diagnostics:
Timeout was reached: [api.opentreeoflife.org] Connection timed out after 10000 milliseconds
--- failed re-building ‘meta-analysis.Rmd’

--- re-building ‘rotl.Rmd’ using rmarkdown
Quitting from lines 64-67 (rotl.Rmd) 
Error: processing vignette 'rotl.Rmd' failed with diagnostics:
Timeout was reached: [api.opentreeoflife.org] Connection timed out after 10001 milliseconds
--- failed re-building ‘rotl.Rmd’

SUMMARY: processing the following files failed:
  ‘data_mashups.Rmd’ ‘meta-analysis.Rmd’ ‘rotl.Rmd’

Error: Vignette re-building failed.
Execution halted
.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.
royston.test: no visible global function definition for ‘shapiro.test’
royston.test: no visible global function definition for ‘cor’
royston.test: no visible global function definition for ‘qnorm’
royston.test: no visible global function definition for ‘pnorm’
royston.test: no visible global function definition for ‘cov’
royston.test: no visible global function definition for ‘mahalanobis’
royston.test: no visible global function definition for ‘qqplot’
royston.test: no visible global function definition for ‘qchisq’
royston.test: no visible global function definition for ‘ppoints’
royston.test: no visible global function definition for ‘abline’
royston.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  abline cor cov mahalanobis pchisq pnorm ppoints qchisq qnorm qqplot
  shapiro.test
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "cor", "cov", "mahalanobis", "pchisq", "pnorm",
             "ppoints", "qchisq", "qnorm", "qqplot", "shapiro.test")
to your NAMESPACE file.
Package in Depends field not imported from: ‘hash’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
P: no visible global function definition for ‘has.key’
get_rand_int: no visible global function definition for ‘runif’
last: no visible global function definition for ‘tail’
rand_partitions: no visible global function definition for ‘hash’
Undefined global functions or variables:
  has.key hash runif tail
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘codelists.Rmd’
'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
Found the following files/directories:
  ‘Rpdb.pdb’
Found the following files/directories:
  ‘mygraph.eps’ ‘mygraph.png’ ‘mygraph.tex’
Found the following files/directories:
  ‘Datasample.mads.txt’ ‘Datasample.medians.txt’ ‘control_plot.pdf’
  ‘correlation_plot.pdf’ ‘dataIII_qqplot.pdf’ ‘kruskalBoxplot.pdf’
  ‘plotQC.pdf’ ‘simpleBoxplot.pdf’ ‘wilcoxonBoxplot.pdf’
but_last: no visible global function definition for ‘head’
first: no visible global function definition for ‘head’
last: no visible global function definition for ‘tail’
preview_frames: no visible global function definition for ‘str’
print.EprimeFrame: no visible global function definition for ‘str’
print.FrameList: no visible global function definition for ‘str’
Undefined global functions or variables:
  head str tail
Consider adding
  importFrom("utils", "head", "str", "tail")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘rpsychi-Ex.R’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rPython.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘rjpod’
Found the following files/directories:
  ‘HL_H0.pdf’ ‘pi0infer.pdf’ ‘rate.txt’ ‘summary.txt’
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.
Found the following files/directories:
  ‘test.bpl’ ‘test.cr’ ‘test.ct’
Package vignette with placeholder title ‘Vignette Title’:
  ‘rescaling_data.Rmd’
'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 ‘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 pnorm printCoefmat pt rnorm
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "grid", "legend",
             "lines", "par")
  importFrom("stats", "dnorm", "median", "model.frame", "model.matrix",
             "model.response", "pnorm", "printCoefmat", "pt", "rnorm")
to your NAMESPACE file.
stripslash: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Running examples in ‘RSDA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: VeterinaryData
> ### Title: Symbolic interval data example
> ### Aliases: VeterinaryData
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(VeterinaryData)
> VeterinaryData
Error in get(x, envir = ns, inherits = FALSE) : 
  object 'warningc' not found
Calls: <Anonymous> ... do.call -> [ -> [.symbolic_tbl -> getFromNamespace -> get
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 40-42 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
object ‘warningc’ not found
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
convexhull: no visible global function definition for ‘chull’
convexhull: no visible global function definition for ‘rnorm’
drawcompletegraph: no visible global function definition for ‘segments’
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 ‘chull’
rsplot: no visible global function definition for ‘polygon’
rsplot: no visible global function definition for ‘points’
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 ‘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 points polygon rnorm runif segments
Consider adding
  importFrom("grDevices", "chull")
  importFrom("graphics", "points", "polygon", "segments")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: ‘Rcompression’
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:
  Rserv.c:2150:3: warning: ‘RSA_generate_key’ is deprecated [-Wdeprecated-declarations]
  Rserv.c:816:4: warning: ignoring return value of ‘setgid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:817:3: warning: ignoring return value of ‘setuid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:820:22: warning: ignoring return value of ‘setgid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:821:22: warning: ignoring return value of ‘setuid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:372:2: warning: ignoring return value of ‘chown’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:375:3: warning: ignoring return value of ‘chown’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:2342:3: warning: ignoring return value of ‘chdir’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:3351:4: warning: ignoring return value of ‘chdir’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:3358:3: warning: ignoring return value of ‘chdir’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:2088:7: warning: ignoring return value of ‘setgid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:2090:7: warning: ignoring return value of ‘setuid’, declared with attribute warn_unused_result [-Wunused-result]
  oc.c:47:5: warning: ‘RAND_pseudo_bytes’ is deprecated [-Wdeprecated-declarations]
  standalone.c:220:3: warning: ignoring return value of ‘chdir’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rserve.Rcheck/00install.out’ for details.
Non-standard files/directories found at top level:
  ‘aclocal.m4’ ‘clients’ ‘clients.txt’ ‘version’
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor 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 ‘points’
sfaClassify: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines par points rainbow rnorm runif sd var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "lines", "par", "points")
  importFrom("stats", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
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.
Found the following files/directories:
  ‘Database’ ‘rSQM.yaml’ ‘rSQM_Sample_Project’ ‘sample_script.R’
Package vignette with placeholder title ‘Vignette Title’:
  ‘main-vignette.Rmd’
Found the following files/directories:
  ‘Rplots.svg’
Found the following files/directories:
  ‘bitmap.jpg’ ‘bitmap.png’ ‘bitmap.webp’ ‘out.pdf’ ‘out.png’ ‘out.ps’
  ‘out.svg’
Found the following files/directories:
  ‘svgplot1.svg’ ‘svgplot10.svg’ ‘svgplot11.svg’ ‘svgplot12.svg’
  ‘svgplot13.svg’ ‘svgplot2.svg’ ‘svgplot3.svg’ ‘svgplot4.svg’
  ‘svgplot5.svg’ ‘svgplot6.svg’ ‘svgplot7.svg’ ‘svgplot8.svg’
  ‘svgplot9.svg’
Found the following files/directories:
  ‘mapCH2017.rda’
Math.Sym: no visible binding for global variable ‘transtab’
jythonStart: no visible global function definition for ‘.jinit’
jythonStart: no visible global function definition for ‘.jnew’
jythonStart: no visible binding for global variable ‘.Jython’
sympy: no visible binding for global variable ‘.Jython’
sympy: no visible global function definition for ‘.jstrVal’
sympyStart: no visible binding for global variable ‘.Jython’
Undefined global functions or variables:
  .Jython .jinit .jnew .jstrVal transtab

Found the following assignments to the global environment:
File ‘rSymPy/R/sympy.R’:
  assign(".Jython", .jnew("org.python.util.PythonInterpreter"), 
    .GlobalEnv)
  assign(".Jython", rJython(modules = system.file("Lib", package = "rSymPy")), 
    .GlobalEnv)
barplot.rtconnect: no visible global function definition for ‘rainbow’
barplot.rtconnect: no visible global function definition for ‘text’
plot.rtconnect: no visible global function definition for ‘par’
plot.rtconnect: no visible global function definition for ‘axis.Date’
rtconnect: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  axis.Date par rainbow read.table text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis.Date", "par", "text")
  importFrom("utils", "read.table")
to your NAMESPACE file.
plotGLCM: no visible global function definition for ‘points’
Undefined global functions or variables:
  points
Consider adding
  importFrom("graphics", "points")
to your NAMESPACE file.
Found the following files/directories:
  ‘test_addPageBreak.doc’ ‘test_addPlot.doc’ ‘test_addSessionInfo.doc’
  ‘test_addTable.doc’
Found the following files/directories:
  ‘Tsttwalk.dat’
Found the following files/directories:
  ‘results’
Found the following files/directories:
  ‘somefile.xml’
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.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RVowpalWabbit.Rcheck/00install.out’ for details.
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
  Output from running autoreconf:
  aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
  configure.in:22: warning: underquoted definition of AC_PROG_R
  configure.in:22:   run info Automake 'Extending aclocal'
  configure.in:22:   or see https://www.gnu.org/software/automake/manual/automake.html#Extending-aclocal
  configure.in:86: warning: the serial number must appear before any macro definition
  configure.in:362: warning: the serial number must appear before any macro definition
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.
Running examples in ‘rwars-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_all_planets
> ### Title: Retrieve Data about Every DB Entry in a Class
> ### Aliases: all_entries get_all_films get_all_people get_all_planets
> ###   get_all_species get_all_starships get_all_vehicles
> 
> ### ** Examples
> 
> #Retrieve all planets, parsing
> planets <- get_all_planets(parse_result = TRUE)
Error in query("/planets/", ...) : Not Found (HTTP 404).
Calls: get_all_planets -> query -> stop_for_status
Execution halted
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’
predict.RWBP: no visible global function definition for ‘head’
Undefined global functions or variables:
  head kmeans model.extract na.omit
Consider adding
  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.
Found the following files/directories:
  ‘RWebLogo.pdf’ ‘RWebLogo.png’
.dwt: no visible global function definition for ‘median’
.udwt: no visible global function definition for ‘median’
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
Consider adding
  importFrom("graphics", "axis", "box", "legend", "lines")
  importFrom("stats", "median")
to your NAMESPACE file.
flemming.plot: no visible global function definition for ‘par’
flemming.plot: no visible global function definition for ‘segments’
flemming.plot: no visible global function definition for ‘text’
flemming.plot : triax.segments: no visible global function definition
  for ‘segments’
legend.bubbles: no visible global function definition for ‘quantile’
legend.bubbles: no visible global function definition for ‘legend’
other.methods: no visible global function definition for ‘quantile’
pejrup.plot: no visible global function definition for ‘par’
pejrup.plot: no visible global function definition for ‘segments’
pejrup.plot: no visible global function definition for ‘text’
pejrup.plot : triax.segments: no visible global function definition for
  ‘segments’
pejrup.plot: no visible global function definition for ‘legend’
rysgran.plot: no visible global function definition for ‘par’
rysgran.plot: no visible global function definition for ‘text’
rysgran.plot: no visible global function definition for ‘points’
rysgran.plot: no visible global function definition for ‘abline’
rysgran.plot: no visible global function definition for ‘mtext’
rysgran.ternary: no visible global function definition for ‘par’
rysgran.ternary: no visible global function definition for ‘points’
rysgran.ternary: no visible global function definition for ‘text’
shepard.plot: no visible global function definition for ‘par’
shepard.plot: no visible global function definition for ‘segments’
shepard.plot: no visible global function definition for ‘text’
shepard.plot : triax.segments: no visible global function definition
  for ‘segments’
shepard.plot: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline legend mtext par points quantile segments text
Consider adding
  importFrom("graphics", "abline", "legend", "mtext", "par", "points",
             "segments", "text")
  importFrom("stats", "quantile")
to your NAMESPACE file.
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.
CV.Epidemic.Vn: no visible global function definition for ‘uniroot’
CV.Epidemic.Wn: no visible global function definition for ‘uniroot’
G.alfa: no visible global function definition for ‘dchisq’
Graf.Diagnostic: no visible global function definition for ‘stepfun’
Graf.Diagnostic: no visible global function definition for ‘title’
Graf.Diagnostic: no visible global function definition for ‘quantile’
Graf.Diagnostic: no visible global function definition for ‘legend’
Graf.Diagnostic: no visible global function definition for ‘arrows’
Graf.Diagnostic: no visible global function definition for ‘par’
Plot.ll: no visible global function definition for ‘segments’
Plot.ll: no visible global function definition for ‘axis’
SemiparChangePoint: no visible global function definition for ‘glm’
SemiparChangePoint: no visible binding for global variable ‘binomial’
SemiparChangePoint: no visible global function definition for
  ‘glm.control’
SemiparChangePoint: no visible global function definition for ‘coef’
Sn.alfa : tempfun: no visible global function definition for ‘dchisq’
Sn.alfa : d.tempfun: no visible global function definition for ‘dchisq’
Zn.alfa : tempfun: no visible global function definition for ‘dchisq’
Zn.alfa : d.tempfun: no visible global function definition for ‘dchisq’
cumsum.test: no visible global function definition for ‘var’
p.OneChange : tempfun: no visible global function definition for
  ‘dchisq’
p.OneChange: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  arrows axis binomial coef dchisq glm glm.control legend par quantile
  segments stepfun title uniroot var
Consider adding
  importFrom("graphics", "arrows", "axis", "legend", "par", "segments",
             "title")
  importFrom("stats", "binomial", "coef", "dchisq", "glm", "glm.control",
             "quantile", "stepfun", "uniroot", "var")
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 ‘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 pnorm qnorm rnorm title
  write.table
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "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.
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.
GraphBinaryForestPlot: no visible global function definition for
  ‘abline’
GraphBinaryForestPlot: no visible global function definition for ‘text’
GraphContinuousForestPlot: no visible global function definition for
  ‘abline’
GraphContinuousForestPlot: no visible global function definition for
  ‘text’
ImputeBinaryEvents: no visible global function definition for ‘rbinom’
ImputeSMD: no visible global function definition for ‘rnorm’
funnelplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline rbinom rnorm text
Consider adding
  importFrom("graphics", "abline", "text")
  importFrom("stats", "rbinom", "rnorm")
to your NAMESPACE file.
generate.sample.core: no visible global function definition for
  ‘predict’
mdh: no visible global function definition for ‘model.frame’
mdh: no visible binding for global variable ‘na.fail’
mdh: no visible global function definition for ‘.getXlevels’
mdh: no visible global function definition for ‘quantile’
mdh: no visible global function definition for ‘hist’
predict.mdh: no visible global function definition for ‘model.frame’
samur: no visible global function definition for ‘predict’
Undefined global functions or variables:
  .getXlevels hist model.frame na.fail predict quantile
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", ".getXlevels", "model.frame", "na.fail", "predict",
             "quantile")
to your NAMESPACE file.
Package suggested but not available for checking: ‘mixer’
Running examples in ‘SanzCircos-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: make_circos_links
> ### Title: make_circos_links
> ### Aliases: make_circos_links
> 
> ### ** Examples
> 
> 
> links_df <- data.frame(chrom = c(rep("chr1", 5), rep("chr2", 5)),
+ band = c(rep("band1", 3), rep("band2", 2), "band1", rep("band2", 4)),
+ link = c(1, 2, 3, 1, 2, 1, 1, 3, 4, 5),
+ start = c(1, 3, 5, 10, 35, 1, 5, 8, 13, 15),
+ end = c(3, 5, 10, 35, 39, 5, 8, 13, 15, 21))
> 
> links <- make_circos_links(links_df, "chrom", "band", "link", "start", "end", status = TRUE)
Warning: `as.tibble()` is deprecated as of tibble 2.0.0.
Please use `as_tibble()` instead.
The signature and semantics have changed, see `?as_tibble`.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Error: Assigned data `as.character(df[[chromosome_grouping]][i])` must be compatible with existing data.
ℹ Error occurred for column `V2`.
✖ Lossy cast from `value` <character> to `x` <logical>.
* Locations: 1.
Backtrace:
     █
  1. └─SanzCircos::make_circos_links(...)
  2.   ├─dplyr::bind_rows(...)
  3.   │ ├─dplyr:::flatten_bindable(dots_values(...))
  4.   │ └─rlang::dots_values(...)
  5.   └─pbapply::pblapply(...)
  6.     └─base::lapply(X, FUN, ...)
  7.       └─SanzCircos:::FUN(X[[i]], ...)
  8.         ├─base::`[<-`(`*tmp*`, 1, 2, value = "chr1")
  9.         └─tibble:::`[<-.tbl_df`(`*tmp*`, 1, 2, value = "chr1")
 10.           └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 11.             └─tibble:::tbl_subassign_row(xj, i, value, value_arg)
 12.               └─base::tryCatch(...)
 13.                 └─base:::tryCatchList(expr, classes, parentenv, handlers)
 14.                   └
Execution halted
Found the following files/directories:
  ‘exemple.QCM.xml’ ‘exemple.VF.xml’ ‘exemple.affichages.xml’
  ‘exemple.categorie.xml’ ‘exemple.image.xml’ ‘exemple.libre.xml’
  ‘exemple.numerique.xml’ ‘exemple.ouverte.xml’ ‘exemple.qroc.xml’
  ‘exemple.question.xml’ ‘exemple.xml’
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.
Found the following files/directories:
  ‘SASPECT.result.txt’
Found the following files/directories:
  ‘stateLung-R01.pdf’ ‘stateLung-R01.txt’
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.
K: no visible global function definition for ‘dnorm’
sBF: no visible global function definition for ‘density’
sBF: no visible global function definition for ‘txtProgressBar’
sBF: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  density dnorm setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "density", "dnorm")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Found the following files/directories:
  ‘insulin_receptor_IR_beta_pY1146_stats.csv’
  ‘insulin_receptor_exp_dataset.csv’ ‘pe_datasets’ ‘pe_plots’
  ‘ps1_datasets’ ‘ps1_plots’ ‘ps2_datasets’ ‘ps2_plots’ ‘sim_datasets’
  ‘sim_datasets_sum’ ‘sim_plots’
Found the following files/directories:
  ‘tdata_R.label’ ‘tdata_R.out’
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.
Missing or unexported objects:
  ‘Rmosek::mosek_lptoprob’ ‘Rmosek::mosek_qptoprob’
Non-standard file/directory found at top level:
  ‘src-java’
ChooseBest: no visible global function definition for ‘head’
GetScores: no visible global function definition for ‘write.table’
ReportTable: no visible binding for global variable ‘sd’
ReportTable: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  head sd write.table
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "head", "write.table")
to your NAMESPACE file.
src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
plot.scair: no visible global function definition for ‘par’
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 ‘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 points rnorm runif
Consider adding
  importFrom("graphics", "par", "points")
  importFrom("stats", "approx", "gaussian", "glm.fit", "rnorm", "runif")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘buildtree.Rmd’
prime.factor: no visible global function definition for ‘data’
prime.factor: no visible binding for global variable ‘primlist’
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘schoolmath/R/prime.factor.R’:
  data(primlist)
See section ‘Good practice’ in ‘?data’.
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.
Found the following files/directories:
  ‘EAP_est1.txt’
CreatePssm: no visible binding for global variable ‘training’
Undefined global functions or variables:
  training
'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.
Found the following calls to attach():
File ‘scriptests/R/source.pkg.R’:
  attach(NULL, pos = pos, name = paste("pkgcode", pkg.name, sep = ":"))
  attach(envir, pos = pos, name = paste("pkgcode", pkg.name, sep = ":"))
See section ‘Good practice’ in ‘?attach’.
Found the following files/directories:
  ‘untitled_consensus_cluster’
lahiri.design: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
estimateTimeToComputeTargetDefinition: no visible global function
  definition for ‘flush.console’
estimateTimeToComputeTargetDefinition: no visible global function
  definition for ‘combn’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘flush.console’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘combn’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘quantile’
initialize,sdcTargetMatrixClass: no visible global function definition
  for ‘flush.console’
Undefined global functions or variables:
  combn flush.console quantile
Consider adding
  importFrom("stats", "quantile")
  importFrom("utils", "combn", "flush.console")
to your NAMESPACE file.
.ACF.compute: no visible global function definition for ‘pnorm’
.ACF.compute: no visible global function definition for ‘qnorm’
.ACF.compute: no visible global function definition for ‘pchisq’
.ACF.plot: no visible global function definition for ‘abline’
.ADF.compute: no visible global function definition for ‘qnorm’
.ADF.compute: no visible global function definition for ‘chisq.test’
.ADF.compute: no visible global function definition for ‘qchisq’
.ADF.compute: no visible global function definition for ‘pchisq’
.ADF.plot: no visible global function definition for ‘abline’
.CADF.plot: no visible global function definition for ‘points’
.DeltaADF.plot: no visible global function definition for ‘abline’
.RPADF.compute: no visible global function definition for ‘pchisq’
.RPADF.compute: no visible global function definition for ‘qchisq’
.RPADF.plot: no visible global function definition for ‘abline’
.RPADF.plot: no visible global function definition for ‘rect’
.fmin: no visible global function definition for ‘optimize’
.fobj: no visible global function definition for ‘pchisq’
.gen.plot: no visible global function definition for ‘axis’
.gen.plot: no visible global function definition for ‘box’
.gen.plot: no visible global function definition for ‘abline’
.lcv: no visible global function definition for ‘bw.nrd0’
.lcv: no visible global function definition for ‘nlm’
ADF: no visible binding for global variable ‘p.adjust.methods’
ADF: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  abline axis box bw.nrd0 chisq.test nlm optimize p.adjust
  p.adjust.methods pchisq pnorm points qchisq qnorm rect
Consider adding
  importFrom("graphics", "abline", "axis", "box", "points", "rect")
  importFrom("stats", "bw.nrd0", "chisq.test", "nlm", "optimize",
             "p.adjust", "p.adjust.methods", "pchisq", "pnorm", "qchisq",
             "qnorm")
to your NAMESPACE file.
Found the following files/directories:
  ‘MC p-value.ps’ ‘Output.csv’ ‘Rh.ps’ ‘Th.ps’ ‘dataratio .Rdata’
  ‘featuresRmax.csv’ ‘featuresT.csv’
dimplot: no visible global function definition for ‘par’
dimplot: no visible global function definition for ‘barplot’
dimplot: no visible global function definition for ‘axis’
find.traj: no visible global function definition for ‘flush.console’
nullprob: no visible global function definition for ‘pbinom’
pbox: no visible global function definition for ‘rect’
pbox: no visible global function definition for ‘par’
prim.traj: no visible global function definition for ‘flush.console’
prim.trajauto: no visible global function definition for
  ‘flush.console’
resampstats: no visible binding for global variable ‘sd’
scatterbox: no visible binding for global variable ‘box’
sd.start: no visible global function definition for ‘read.csv’
sd.start: no visible global function definition for ‘par’
sd.start: no visible global function definition for ‘graphics.off’
sd.start: no visible global function definition for ‘hist’
sd.start: no visible global function definition for ‘plot.ecdf’
sd.start: no visible global function definition for ‘write.csv’
sd.start: no visible global function definition for ‘flush.console’
trajplot: no visible global function definition for ‘points’
trajplot: no visible global function definition for ‘flush.console’
trajplot: no visible global function definition for ‘lm’
trajplot: no visible global function definition for ‘predict.lm’
trajplot: no visible global function definition for ‘identify’
Undefined global functions or variables:
  axis barplot box flush.console graphics.off hist identify lm par
  pbinom plot.ecdf points predict.lm read.csv rect sd write.csv
Consider adding
  importFrom("grDevices", "graphics.off")
  importFrom("graphics", "axis", "barplot", "box", "hist", "identify",
             "par", "points", "rect")
  importFrom("stats", "lm", "pbinom", "plot.ecdf", "predict.lm", "sd")
  importFrom("utils", "flush.console", "read.csv", "write.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘demofile.txt’
Package in Depends field not imported from: ‘lars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
sealasso: no visible global function definition for ‘lars’
weight.calc: no visible global function definition for ‘lars’
Undefined global functions or variables:
  lars
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 ‘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 ‘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 points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "points")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘seastests-vignette.Rmd’
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.
Found the following files/directories:
  ‘examplePlots0404104041.pdf’ ‘myfit104035.pdf’ ‘myfit104037.pdf’
  ‘myfit104041.pdf’ ‘myfit1_survregCall.txt’ ‘myfit304041.pdf’
  ‘myfit3_survregCall.txt’
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 ‘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 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",
             "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.
Running examples in ‘secret-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_travis_user
> ### Title: Add a user via their Travis repo.
> ### Aliases: add_travis_user
> 
> ### ** Examples
> 
> vault <- file.path(tempdir(), ".vault")
> create_vault(vault)
> 
> add_travis_user("gaborcsardi/secret", vault = vault)
Error in open.connection(con, "rb") : HTTP error 404.
Calls: add_travis_user ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
Execution halted
src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
Package suggested but not available for checking: ‘rsbml’
.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.
Found the following files/directories:
  ‘testrun1.dic’ ‘testrun1.txt’ ‘testrun2.dic’ ‘testrun2.txt’
Found the following files/directories:
  ‘SM-Ex-H04 GA Co 2010 hatch-ge mean popdens-d15 a60.pdf’ ‘SM-Ex-c30
  Kentucky All Co Map w hatching-defaults.pdf’ ‘SM-Ex-c64 GA
  Counties10-PC age 65 and up-def.pdf’
  ‘SM-Ex-c80-WashBalt-County-CSA-def.pdf’ ‘SM-Ex-s01 States Map of
  Cancer Mortality-defaults.pdf’ ‘SM-Ex-s02 States Map of Cancer
  Mortality-w hatching.pdf’ ‘SM-Ex-sr11 Seer Reg 17 Map stB-A
  srB-D.pdf’ ‘SM-Ex-tr74-WA-Dem-All-Census-Tracts-PCgt65-def.pdf’
  ‘SM-Ex-tr78-WA-Dem-P-Tract-trB-sr.pdf’
Found the following files/directories:
  ‘SeerMapperRegs00-Test-Res.pdf’
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.
Found the following files/directories:
  ‘expression.csv’ ‘group.csv’
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’
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 predict runif splinefun uniroot
Consider adding
  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.
Found the following files/directories:
  ‘Rprof.out’
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’
Package vignette with placeholder title ‘Vignette Title’:
  ‘semPower.Rmd’
Package vignette with placeholder title ‘Vignette Title’:
  ‘introduction-to-package-SEMrushR-.Rmd’
.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 files/directories:
  ‘assocpointpair_result.csv’ ‘foundereffectfinder_result.csv’
  ‘getfreqs_result.csv’ ‘getfreqs_result.png’ ‘orPlot.pdf1_1.pdf’
  ‘orPlot.pdf2_1.pdf’ ‘orPlot.pdf3_1.pdf’ ‘orPlot.pdf4_1.pdf’
  ‘orPlot.pdf5_1.pdf’ ‘orPlot.pdf6_1.pdf’ ‘orPlot.pdf7_1.pdf’
  ‘orPlot.pdf8_1.pdf’ ‘q-values_result.csv’ ‘rewritetuple_result.csv’
  ‘tartan_plot.pdf’ ‘vispair_plot.pdf’ ‘vispairfeat_plot.pdf’
  ‘volcano_plot.pdf’
plotenz : addmark: no visible global function definition for ‘par’
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 segments text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "layout", "par", "segments", "text")
to your NAMESPACE file.
Found the following files/directories:
  ‘total’
capture: no visible binding for global variable ‘resultText’
restore.session: no visible binding for global variable
  ‘.save.session.packages’
restore.session: no visible binding for global variable
  ‘.save.session.search’
save.session: no visible global function definition for ‘dev.list’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.search’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.packages’
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.

Found the following calls to attach():
File ‘session/R/session.R’:
  attach(sub("file:", "", i))
See section ‘Good practice’ in ‘?attach’.
Found the following files/directories:
  ‘RSession.Rda’
setpath: no visible global function definition for ‘cov’
setpath: no visible global function definition for ‘median’
setpath: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cov median pchisq
Consider adding
  importFrom("stats", "cov", "median", "pchisq")
to your NAMESPACE file.
random.number.test: no visible global function definition for ‘runif’
random.number.test: no visible global function definition for ‘rnorm’
setRNG: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Package unavailable to check Rd xrefs: ‘loomR’
Unknown package ‘SDMTools’ in Rd xrefs
'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.
.computePStar: no visible global function definition for ‘uniroot’
plotBoundary: no visible global function definition for
  ‘scale_y_continuous’
Undefined global functions or variables:
  scale_y_continuous uniroot
Consider adding
  importFrom("stats", "uniroot")
to your NAMESPACE file.
amse: no visible global function definition for ‘na.omit’
arb: no visible global function definition for ‘na.omit’
rdatagen: no visible global function definition for ‘qnorm’
rdatagen: no visible global function definition for ‘pbinom’
rdatagen: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  na.omit pbinom pnorm qnorm
Consider adding
  importFrom("stats", "na.omit", "pbinom", "pnorm", "qnorm")
to your NAMESPACE file.
'library' or 'require' call to ‘foreign’ which was already attached by Depends.
  Please remove these calls from your code.
Package suggested but not available for checking: ‘hydromad’
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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘SI.Rmd’
Found the following files/directories:
  ‘.shiny_run’ ‘shinyShortcut.desktop’
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.
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 ‘points’
plot.verify.ho: no visible global function definition for ‘points’
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 points predict princomp rnorm
  var
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "cor", "cov", "predict", "princomp", "rnorm",
             "var")
to your NAMESPACE file.
Found the following files/directories:
  ‘3_FindHaplo_Example2_modified.txt’
  ‘4_Example3_HapPerPop_Weighted.txt’
  ‘4_Example3_IndelDistanceMatrixMullerMod.txt’
  ‘4_FindHaplo_Example2_modified.txt’ ‘FindHaplo.txt’
  ‘Haplotypes_DefaultNames.txt’ ‘Haplotypes_sequentialNames.txt’
  ‘Interaction.txt’ ‘Modules_summary.txt’
  ‘NINA.ThresholdEstimation.txt’ ‘NINA_Network.pdf’ ‘Network.pdf’
  ‘PercThr Estimation.pdf’ ‘PercThresholdEstimation.txt’
  ‘PercolatedNetwork.pdf’ ‘PopulationDistances.r.txt’ ‘Weighted.txt’
  ‘ex1.fas’ ‘ex2.2.fas’ ‘ex2.fas’ ‘ex2_unique.fas’ ‘ex3.fas’
  ‘simulated_sequences_rep1.fas’ ‘simulated_sequences_rep2.fas’
  ‘simulated_sequences_tips_rep1.fas’
  ‘simulated_sequences_tips_rep2.fas’
dSepAdji: no visible global function definition for ‘as’
dag2cpdagAdj: no visible global function definition for ‘as’
randomDAG: no visible global function definition for ‘rbinom’
structIntervDist: no visible global function definition for ‘as’
Undefined global functions or variables:
  as rbinom
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "rbinom")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘MM.csv’ ‘Simul.csv’ ‘catalytic.csv’
.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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘animate.Rmd’ using rmarkdown
--- finished re-building ‘animate.Rmd’

--- re-building ‘buttons.Rmd’ using rmarkdown
--- finished re-building ‘buttons.Rmd’

--- re-building ‘cluster.Rmd’ using rmarkdown
--- finished re-building ‘cluster.Rmd’

--- re-building ‘dynamic.Rmd’ using rmarkdown
Quitting from lines 27-45 (dynamic.Rmd) 
Error: processing vignette 'dynamic.Rmd' failed with diagnostics:
Assigned data `runif(15, 500, 750)` must be compatible with existing data.
✖ Existing data has 75 rows.
✖ Assigned data has 15 rows.
ℹ Only vectors of size 1 are recycled.
--- failed re-building ‘dynamic.Rmd’

--- re-building ‘formats.Rmd’ using rmarkdown
--- finished re-building ‘formats.Rmd’

--- re-building ‘get_started.Rmd’ using rmarkdown
--- finished re-building ‘get_started.Rmd’

--- re-building ‘layout.Rmd’ using rmarkdown
--- finished re-building ‘layout.Rmd’

--- re-building ‘plugins.Rmd’ using rmarkdown
--- finished re-building ‘plugins.Rmd’

--- re-building ‘settings.Rmd’ using rmarkdown
--- finished re-building ‘settings.Rmd’

--- re-building ‘shiny.Rmd’ using rmarkdown
--- finished re-building ‘shiny.Rmd’

--- re-building ‘talkcross.Rmd’ using rmarkdown
--- finished re-building ‘talkcross.Rmd’

SUMMARY: processing the following file failed:
  ‘dynamic.Rmd’

Error: Vignette re-building failed.
Execution halted
Package vignette with placeholder title ‘Vignette Title’:
  ‘getting-started.Rmd’
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.
Found the following files/directories:
  ‘ExportFigtree1.tre’
'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 ‘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 predict
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "approx", "predict")
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.
Found the following files/directories:
  ‘database.csv’ ‘output.csv’ ‘output_clst.csv’
Found the following files/directories:
  ‘res_mutation.tsv’ ‘res_mutationCounts.txt’
  ‘res_processContribution.txt’ ‘res_processes.txt’
cumallcausehr: no visible global function definition for ‘integrate’
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 ‘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’
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 polygon rnorm
  runif uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "polygon")
  importFrom("stats", "confint", "integrate", "model.matrix", "rnorm",
             "runif", "uniroot")
to your NAMESPACE file.
Found the following files/directories:
  ‘simu.pheno’ ‘usedpars.txt’
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘HISTORY’
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 ‘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 ‘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 quantile setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "abline", "legend", "par")
  importFrom("stats", "lm", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Found the following files/directories:
  ‘SimRAD-exampleRefSeq-Fasta.fa’ ‘SimRAD-exampleRefSeq.fa’
Running ‘testthat.R’ [4s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(simrel)
  > 
  > test_check("simrel")
  ── 1. Error: Prepare Design (@test-utils.R#44)  ────────────────────────────────
  Can't join on 'q' x 'q' because of incompatible types (list / list)
  Backtrace:
   1. testthat::expect_identical(prepare_design(opts), dgn)
   3. testthat:::compare.default(act$val, exp$val)
   5. dplyr:::all.equal.tbl_df(x, y, ...)
   6. dplyr:::equal_data_frame(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 169 | SKIPPED: 21 | WARNINGS: 3 | FAILED: 1 ]
  1. Error: Prepare Design (@test-utils.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following files/directories:
  ‘crop_device.pdf’
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
plotBGpvalues: no visible global function definition for ‘par’
plotBGpvalues: no visible global function definition for ‘title’
plotBGpvalues: no visible global function definition for ‘axis’
plotBGpvalues: no visible binding for global variable ‘abline’
plotBGpvalues: no visible global function definition for ‘box’
plotCGpvalues: no visible global function definition for ‘par’
plotCGpvalues: no visible global function definition for ‘title’
plotCGpvalues: no visible global function definition for ‘axis’
plotCGpvalues: no visible binding for global variable ‘abline’
plotCGpvalues: no visible global function definition for ‘box’
plotDAGpvalues: no visible global function definition for ‘par’
plotDAGpvalues: no visible global function definition for ‘title’
plotDAGpvalues: no visible global function definition for ‘axis’
plotDAGpvalues: no visible binding for global variable ‘abline’
plotDAGpvalues: no visible global function definition for ‘box’
plotUGpvalues: no visible global function definition for ‘par’
plotUGpvalues: no visible global function definition for ‘title’
plotUGpvalues: no visible global function definition for ‘axis’
plotUGpvalues: no visible binding for global variable ‘abline’
plotUGpvalues: no visible global function definition for ‘box’
simpvalueVec: no visible binding for global variable ‘pnorm’
sinBG: no visible global function definition for ‘cov2cor’
sinCG : sinAMP: no visible global function definition for ‘cov2cor’
sinCG : sinLWF: no visible global function definition for ‘cov2cor’
sinDAG: no visible global function definition for ‘cov2cor’
sinUG: no visible global function definition for ‘cov2cor’
Undefined global functions or variables:
  abline axis box cov2cor par pnorm title
Consider adding
  importFrom("graphics", "abline", "axis", "box", "par", "title")
  importFrom("stats", "cov2cor", "pnorm")
to your NAMESPACE file.
Found the following files/directories:
  ‘agency.csv’ ‘calendar.csv’ ‘routes.txt’ ‘shapes.txt’
  ‘stop_times.txt’ ‘stops.txt’ ‘translations.txt’ ‘trips.txt’
Found the following files/directories:
  ‘helicopter.pdf’
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.
slcestimates: no visible global function definition for ‘par’
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 points title
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "par", "points",
             "title")
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.
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 ‘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 pnorm survreg var
Consider adding
  importFrom("graphics", "lines", "matplot")
  importFrom("stats", "model.extract", "model.frame", "model.matrix",
             "na.omit", "optim", "pnorm", "var")
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 ‘text’
plot.imds: no visible global function definition for ‘rect’
Undefined global functions or variables:
  as.dist cmdscale dist lines optim rect runif text
Consider adding
  importFrom("graphics", "lines", "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.
lines.SmithWilsonYieldCurve: no visible global function definition for
  ‘lines’
points.SmithWilsonYieldCurve: no visible global function definition for
  ‘points’
Undefined global functions or variables:
  lines points
Consider adding
  importFrom("graphics", "lines", "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 files/directories:
  ‘my_new_social_media_plot.png’
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.
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.
Found the following files/directories:
  ‘geneSet.set’ ‘snplistdb.sqlite’
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.
Packages in Depends field not imported from:
  ‘colorspace’ ‘snpStats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
check.args: no visible global function definition for ‘is’
write.sbams: no visible global function definition for ‘as’
write.sbams: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  as is write.table
Consider adding
  importFrom("methods", "as", "is")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following calls to attach():
File ‘SOAR/R/SOAR.R’:
  attach(NULL, pos, basename(directory))
See section ‘Good practice’ in ‘?attach’.
Found the following files/directories:
  ‘.R_Test’
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.
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.
compileDatabase: no visible global function definition for ‘use_data’
Undefined global functions or variables:
  use_data
Package vignette with placeholder title ‘Vignette Title’:
  ‘SolveRationalMatrixEquation.Rmd’
soma: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  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.
Non-standard files/directories found at top level:
  ‘README.markdown’ ‘build_package.sh’ ‘upload.sh’
Found the following files/directories:
  ‘asc.gif’ ‘bg.gif’ ‘desc.gif’ ‘jquery-1.4.2.js’
  ‘jquery.tablesorter.js’ ‘sample.html’ ‘style.css’
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.
Found the following files/directories:
  ‘splineSearch.xls’
Package suggested but not available for checking: ‘SciencesPo’
Package suggested but not available for checking: ‘r2cytoscape’
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 pnorm qnorm rbinom rexp runif
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("stats", "constrOptim", "optim", "pnorm", "qnorm", "rbinom",
             "rexp", "runif", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
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.
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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘Starting.Rmd’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SpatialPosition.Rcheck/00install.out’ for details.
Running examples in ‘spatial.tools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tahoe_highrez_training
> ### Title: Point and polygon files for use with spatial.tools
> ### Aliases: tahoe_highrez_training
> ### Keywords: data
> 
> ### ** Examples
> 
> library("raster")
Loading required package: sp
> library("rgdal")
rgdal: version: 1.4-8, (SVN revision 845)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 3.0.4, released 2020/01/28
 Path to GDAL shared files: 
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 7.0.0, March 1st, 2020, [PJ_VERSION: 700]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.4-1 
> tahoe_highrez_training_polygons <- readOGR(
+ 	dsn=system.file("external", package="spatial.tools"),layer="tahoe_highrez_training")
OGR data source with driver: ESRI Shapefile 
Source: "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/spatial.tools/external", layer: "tahoe_highrez_training"
with 8 features
It has 2 fields
> spplot(tahoe_highrez_training_polygons,zcol="Class")
Warning in extend.limits(range(as.numeric(z), finite = TRUE)) :
  NAs introduced by coercion
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 seq.default(zrng[1], zrng[2], length.out = cuts + 2) : 
  'from' must be a finite number
Calls: spplot ... <Anonymous> -> levelplot.formula -> seq -> seq.default
Execution halted
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.
'library' or 'require' call to ‘leaps’ which was already attached by Depends.
  Please remove these calls from your code.
modSearch: no visible global function definition for ‘glm’
modSearch: no visible binding for global variable ‘binomial’
modSearch: no visible global function definition for ‘na.omit’
modSearch: no visible global function definition for ‘as.formula’
speff: no visible binding for global variable ‘na.pass’
speff: no visible global function definition for ‘model.matrix’
speff: no visible global function definition for ‘terms’
speff: no visible global function definition for ‘model.response’
speff: no visible global function definition for ‘as.formula’
speff: no visible global function definition for ‘predict’
speff: no visible global function definition for ‘na.omit’
speff: no visible global function definition for ‘glm’
speff: no visible binding for global variable ‘na.omit’
speffSurv: no visible global function definition for ‘model.matrix’
speffSurv: no visible global function definition for ‘terms’
speffSurv: no visible global function definition for ‘model.response’
speffSurv: no visible global function definition for ‘as.formula’
speffSurv: no visible global function definition for ‘uniroot’
summary.speff: no visible global function definition for ‘qnorm’
summary.speff: no visible global function definition for ‘pnorm’
summary.speffSurv: no visible global function definition for ‘qnorm’
summary.speffSurv: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula binomial glm model.matrix model.response na.omit na.pass
  pnorm predict qnorm terms uniroot
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "model.matrix",
             "model.response", "na.omit", "na.pass", "pnorm", "predict",
             "qnorm", "terms", "uniroot")
to your NAMESPACE file.
Found the following files/directories:
  ‘.neig’
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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘spiders.Rmd’
Found the following files/directories:
  ‘AlphaGA_3.txt’ ‘AlphaML_3.txt’ ‘BetaGA_3.txt’ ‘BetaML_3.txt’
  ‘Performance_GA_ML_ 3 .pdf’ ‘SPIGA_3Pmon.Pm_St1.pdf’
  ‘SPIGA_3Pmon.Pm_St2.pdf’ ‘SPI_AG_3.txt’ ‘SPI_ML_3.txt’
  ‘SPI_ML_3Pm_St1.pdf’ ‘SPI_ML_3Pm_St2.pdf’ ‘SPI_ML_3Pm_St3.pdf’
  ‘SPI_ML_3Pm_St4.pdf’ ‘SPI_PARAM_3.txt’ ‘SPI_PARAM_3Pm_St1.pdf’
  ‘SPI_PARAM_3Pm_St2.pdf’ ‘SPI_PARAM_3Pm_St3.pdf’
  ‘SPI_PARAM_3Pm_St4.pdf’
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.
Package suggested but not available for checking: ‘mbgraphic’
'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.
Found the following files/directories:
  ‘spi.txt’
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’
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 qchisq quantile runif
Consider adding
  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.
Missing or unexported objects:
  ‘rgdal::checkCRSArgs_ng’ ‘rgdal::new_proj_and_gdal’
Package vignette with placeholder title ‘Vignette Title’:
  ‘spreadr_vignette.Rmd’
plot.SPRT: no visible global function definition for ‘par’
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
Consider adding
  importFrom("graphics", "abline", "par")
  importFrom("utils", "head")
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.
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.
Running ‘testthat.R’ [17s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > #    Copyright 2015 Province of British Columbia
  > #
  > #    Licensed under the Apache License, Version 2.0 (the "License");
  > #    you may not use this file except in compliance with the License.
  > #    You may obtain a copy of the License at
  > #
  > #       http://www.apache.org/licenses/LICENSE-2.0
  > #
  > #    Unless required by applicable law or agreed to in writing, software
  > #    distributed under the License is distributed on an "AS IS" BASIS,
  > #    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  > #    See the License for the specific language governing permissions and
  > #    limitations under the License.
  > 
  > library(testthat)
  > library(ssdtools)
  
  Attaching package: 'ssdtools'
  
  The following objects are masked from 'package:stats':
  
      dgamma, dweibull, pgamma, pweibull, qgamma, qweibull, rgamma,
      rweibull
  
  > 
  > test_check("ssdtools")
  ── 1. Failure: ssd_gof fitdistscens (@test-gof.R#46)  ──────────────────────────
  as.data.frame(ssd_gof(fluazinam_dists)) not equal to structure(...).
  Attributes: < Component "row.names": Modes: numeric, character >
  Attributes: < Component "row.names": target is numeric, current is character >
  
  ── 2. Failure: manual (@test-schwarz-tillmans.R#24)  ───────────────────────────
  as.data.frame(ssd_gof(dists)) not equal to structure(...).
  Attributes: < Component "row.names": Modes: numeric, character >
  Attributes: < Component "row.names": target is numeric, current is character >
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 269 | SKIPPED: 0 | WARNINGS: 12 | FAILED: 2 ]
  1. Failure: ssd_gof fitdistscens (@test-gof.R#46) 
  2. Failure: manual (@test-schwarz-tillmans.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
L_hNV: no visible global function definition for ‘pnorm’
L_hNV_rho: no visible global function definition for ‘pnorm’
eff.ssfa: no visible global function definition for ‘pnorm’
plot_fitted: no visible global function definition for ‘lines’
plot_moran: no visible global function definition for ‘residuals’
print.summary.ssfa: no visible global function definition for
  ‘printCoefmat’
ssfa: no visible global function definition for ‘model.frame’
ssfa: no visible global function definition for ‘model.response’
ssfa.fit: no visible global function definition for ‘lm’
ssfa.fit: no visible global function definition for ‘var’
ssfa.fit: no visible global function definition for ‘logLik’
summary.ssfa: no visible global function definition for ‘pnorm’
summary.ssfa: no visible global function definition for ‘logLik’
summary.ssfa: no visible global function definition for ‘pchisq’
summary.ssfa: no visible binding for global variable ‘df’
u.ssfa: no visible global function definition for ‘dnorm’
u.ssfa: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  df dnorm lines lm logLik model.frame model.response pchisq pnorm
  printCoefmat residuals var
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "df", "dnorm", "lm", "logLik", "model.frame",
             "model.response", "pchisq", "pnorm", "printCoefmat",
             "residuals", "var")
to your NAMESPACE file.
Package in Depends field not imported from: ‘survey’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fit.model: no visible global function definition for ‘hadamard’
Undefined global functions or variables:
  hadamard
mem.usage: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  read.delim
Consider adding
  importFrom("utils", "read.delim")
to your NAMESPACE file.
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.
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.
.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 ‘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 ‘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 png
  rainbow tiff
Consider adding
  importFrom("grDevices", "dev.copy2eps", "dev.copy2pdf", "dev.new",
             "dev.print", "png", "rainbow", "tiff")
  importFrom("graphics", "legend", "lines", "par")
to your NAMESPACE file.
Found the following files/directories:
  ‘Rplot001.pdf’
Non-standard file/directory found at top level:
  ‘Licence’
'library' or 'require' calls to packages already attached by Depends:
  ‘np’ ‘sp’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘np’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
stkde: no visible global function definition for ‘npudensbw’
stkde: no visible global function definition for ‘npudens’
stkde: no visible global function definition for ‘quantile’
stkde: no visible global function definition for ‘heat.colors’
stkde: no visible global function definition for ‘par’
stkde: no visible global function definition for ‘image’
stkde: no visible global function definition for ‘contour’
stkde.base: no visible global function definition for ‘npudensbw’
stkde.base: no visible global function definition for ‘npudens’
stkde.sig: no visible global function definition for ‘SpatialPoints’
stkde.sig: no visible global function definition for ‘spsample’
stkde.sig: no visible global function definition for ‘bbox’
stkde.sig: no visible global function definition for ‘quantile’
stkde.sig: no visible global function definition for ‘heat.colors’
stkde.sig: no visible global function definition for ‘par’
stkde.sig: no visible global function definition for ‘image’
stkde.sig: no visible global function definition for ‘contour’
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.

Found the following calls to attach():
File ‘stam/R/stkde.sig.r’:
  attach(samdata)
See section ‘Good practice’ in ‘?attach’.
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.
Package which this enhances but not available for checking: ‘Zelig’
'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.
Package suggested but not available for checking: ‘starsdata’
Unexported objects imported by ':::' calls:
  ‘s2dverification:::.KnownLatNames’ ‘s2dverification:::.KnownLonNames’
  See the note in ?`:::` about the use of this operator.
Found the following files/directories:
  ‘testmat.sdml’ ‘testmat2.sdml’
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 ‘lines’
auc: no visible global function definition for ‘par’
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 ‘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 ‘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 quantile sd
Consider adding
  importFrom("graphics", "abline", "lines", "par")
  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.
Running examples in ‘statsr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bandit_posterior
> ### Title: bandit posterior
> ### Aliases: bandit_posterior
> 
> ### ** Examples
> 
> data = data.frame(machine = c(1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L), 
+                   outcome = c("W", "L", "W", "L", "L", "W", "L", "L", "L", "W"))
> bandit_posterior(data)
m1_good m2_good 
    0.5     0.5 
> plot_bandit_posterior(data)
Warning: `data_frame()` is deprecated as of tibble 1.1.0.
Please use `tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Error: Assigned data `prior` must be compatible with row subscript `1`.
✖ 1 row must be assigned.
✖ Assigned data has 2 rows.
ℹ Only vectors of size 1 are recycled.
Backtrace:
    █
 1. └─statsr::plot_bandit_posterior(data)
 2.   ├─base::`[<-`(...)
 3.   └─tibble:::`[<-.tbl_df`(...)
 4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 5.       └─tibble:::vectbl_recycle_rhs(...)
 6.         └─base::tryCatch(...)
 7.           └─base:::tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)
Execution halted
getStp: no visible global function definition for ‘lm’
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 quantile var
Consider adding
  importFrom("grDevices", "as.graphicsAnnot")
  importFrom("graphics", "abline", "axis", "box", "legend")
  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.
Found the following files/directories:
  ‘corrviz.html’
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.
Found the following files/directories:
  ‘myNewStrat.R’
Missing or unexported object: ‘limma::ebayes’
Package vignette with placeholder title ‘Vignette Title’:
  ‘strider.Rmd’
Package suggested but not available for checking: ‘STRaitRazoR’
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
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').
Found the following files/directories:
  ‘EmiStatR_output’ ‘ExamplePlot-event.pdf’ ‘ExamplePlot-season.pdf’
  ‘Output1_MC-uncertainty_360min-event.pdf’
  ‘Output1_MC-uncertainty_360min-season.pdf’ ‘gof.RData’ ‘gof.csv’
  ‘gofGoF_results.RData’ ‘gofGoF_results.csv’ ‘mc.RData’ ‘sim1.RData’
  ‘summ.RData’ ‘variance.RData’
identifyGraph: no visible global function definition for ‘phyper’
mytriangle: no visible global function definition for ‘symbols’
plotGraph: no visible global function definition for ‘par’
updateOrgEnvir: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  par phyper read.table symbols
Consider adding
  importFrom("graphics", "par", "symbols")
  importFrom("stats", "phyper")
  importFrom("utils", "read.table")
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.
'library' or 'require' call to ‘tkrplot’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
playSudoku : replot: no visible global function definition for ‘par’
playSudoku : replot: no visible global function definition for
  ‘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 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", "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.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 uniroot
Consider adding
  importFrom("stats", "anova", "lm", "model.frame", "optimize",
             "uniroot")
to your NAMESPACE file.
Found the following files/directories:
  ‘CFH.scores.full.vcf’
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.
.p.1gen: warning in formatC(id, wid = 6): partial argument match of
  ‘wid’ to ‘width’
.p.1gen: warning in formatC(s, wid = 4): partial argument match of
  ‘wid’ to ‘width’
.p.1gen: warning in formatC(format(c(round(m, digits = digits),
  0.735))[1], wid = 7, dig = 3): partial argument match of ‘dig’ to
  ‘digits’
.p.1gen: warning in formatC(format(c(round(m, digits = digits),
  0.735))[1], wid = 7, dig = 3): partial argument match of ‘wid’ to
  ‘width’
predict.pelora: warning in matrix(c((1/(1 + exp(-(X[, 1:(noc[i] + 1)]
  %*% koeff))))), nc = 1): partial argument match of ‘nc’ to ‘ncol’
ridge.coef: warning in diag(apply(X, 2, var) * lambda * nrow(X), nr =
  ncol(X)): partial argument match of ‘nr’ to ‘nrow’
aggtrees: no visible global function definition for ‘predict’
coef.pelora: no visible global function definition for ‘fitted’
dlda: no visible binding for global variable ‘var’
logreg: no visible global function definition for ‘glm’
logreg: no visible binding for global variable ‘binomial’
logreg: no visible global function definition for ‘predict’
plot.pelora: no visible global function definition for ‘text’
plot.wilma: no visible global function definition for ‘fitted’
plot.wilma: no visible global function definition for ‘text’
predict.pelora: no visible global function definition for ‘fitted’
predict.pelora: no visible global function definition for ‘coef’
predict.wilma: no visible global function definition for ‘fitted’
print.wilma: no visible global function definition for ‘fitted’
ridge.coef: no visible binding for global variable ‘var’
sign.change: no visible binding for global variable ‘cov’
standardize.genes: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  binomial coef cov fitted glm predict sd text var
Consider adding
  importFrom("graphics", "text")
  importFrom("stats", "binomial", "coef", "cov", "fitted", "glm",
             "predict", "sd", "var")
to your NAMESPACE file.
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.
'library' or 'require' call to ‘gam’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
TrainSuperMDS: no visible global function definition for ‘rnorm’
TrainSuperMDSOnce: no visible global function definition for ‘cmdscale’
TrainSuperMDSOnce: no visible global function definition for ‘quantile’
distmat: no visible global function definition for ‘dist’
Undefined global functions or variables:
  cmdscale dist quantile rnorm
Consider adding
  importFrom("stats", "cmdscale", "dist", "quantile", "rnorm")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

plot.survAUC: no visible global function definition for ‘lines’
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 predict survfit
Consider adding
  importFrom("graphics", "lines")
  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.
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 ‘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 pnorm points qnorm qt runif var
Consider adding
  importFrom("graphics", "par", "points")
  importFrom("stats", "cor", "model.frame", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file.
AER: no visible binding for global variable ‘survexp.fr’
AER: no visible global function definition for ‘na.omit’
AER: no visible global function definition for ‘survexp’
AER: no visible global function definition for ‘poisson’
AER: no visible global function definition for ‘glm’
AER: no visible global function definition for ‘qnorm’
LR: no visible binding for global variable ‘survexp.fr’
LR: no visible global function definition for ‘na.omit’
LR: no visible global function definition for ‘survexp’
LR: no visible global function definition for ‘pchisq’
SMR: no visible binding for global variable ‘survexp.fr’
SMR: no visible global function definition for ‘na.omit’
SMR: no visible global function definition for ‘survexp’
SMR: no visible global function definition for ‘qnorm’
SMR: no visible global function definition for ‘pchisq’
SMR: no visible global function definition for ‘glm’
SMR: no visible binding for global variable ‘poisson’
survexp_plot: no visible binding for global variable ‘survexp.fr’
survexp_plot: no visible global function definition for ‘na.omit’
survexp_plot: no visible global function definition for ‘par’
survexp_plot: no visible global function definition for ‘survfit’
survexp_plot: no visible global function definition for ‘survexp’
survexp_plot: no visible global function definition for ‘lines’
survexp_plot: no visible global function definition for ‘legend’
survexp_plot: no visible global function definition for ‘curve’
survexp_plot: no visible global function definition for ‘arrows’
survexp_plot: no visible global function definition for ‘points’
Undefined global functions or variables:
  arrows curve glm legend lines na.omit par pchisq points poisson qnorm
  survexp survexp.fr survfit
Consider adding
  importFrom("graphics", "arrows", "curve", "legend", "lines", "par",
             "points")
  importFrom("stats", "glm", "na.omit", "pchisq", "poisson", "qnorm")
to your NAMESPACE file.
'library' or 'require' call to ‘survival’ which was already attached by Depends.
  Please remove these calls from your code.
Survgini: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘survC1’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Est.HR.FUN: no visible global function definition for ‘coxph’
Est.HR.FUN: no visible global function definition for ‘basehaz’
Est.HR.FUN: no visible global function definition for ‘approx’
Ghat.FUN: no visible global function definition for ‘survfit’
IDI.INF: no visible global function definition for ‘kmcens’
IDI.INF: no visible global function definition for ‘quantile’
IDI.INF.GRAPH: no visible global function definition for ‘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 points polygon quantile rexp
  survfit title
Consider adding
  importFrom("graphics", "abline", "lines", "points", "polygon", "title")
  importFrom("stats", "approx", "quantile", "rexp")
to your NAMESPACE file.
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’
Undefined global functions or variables:
  alarm
Consider adding
  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/svmpath.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi30spec.o’, ‘mi35mps.o’,
      ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘_gfortran_st_rewind’, possibly from ‘rewind’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi10unix.o’, ‘mi35mps.o’, ‘mi40bfil.o’
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’

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.
.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 ‘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 predict quantile
Consider adding
  importFrom("graphics", "abline", "arrows")
  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.
Package suggested but not available for checking: ‘swephRdata’
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.
Warning in min(matches) :
  no non-missing arguments to min; returning Inf
Warning in getBiocvrFromRvr(myyaml) :
  NAs introduced by coercion to integer range
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘SWMPrExtension-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: seasonal_dot
> ### Title: Seasonal Dot Plot
> ### Aliases: seasonal_dot seasonal_dot.swmpr
> 
> ### ** Examples
> 
> dat_wq <- elksmwq
> #dat_wq <- subset(dat_wq, subset = c('2010-01-01 0:00', '2017-01-01 0:00'))
> dat_wq <- qaqc(dat_wq, qaqc_keep = c(0, 3, 5))
> 
> x <-
+   seasonal_dot(dat_wq, param = 'do_mgl'
+                , lm_trend = TRUE
+                , lm_lab = TRUE
+                , plot_title = TRUE)
Error: Aesthetics must be either length 1 or the same as the data (48): y
Backtrace:
    █
 1. ├─SWMPrExtension::seasonal_dot(...)
 2. └─SWMPrExtension:::seasonal_dot.swmpr(...)
 3.   ├─ggplot2::ggplot_build(plt)
 4.   └─ggplot2:::ggplot_build.ggplot(plt)
 5.     └─ggplot2:::by_layer(function(l, d) l$compute_aesthetics(d, plot))
 6.       └─ggplot2:::f(l = layers[[i]], d = data[[i]])
 7.         └─l$compute_aesthetics(d, plot)
 8.           └─ggplot2:::f(..., self = self)
 9.             └─ggplot2:::check_aesthetics(evaled, n)
Execution halted
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.
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.
'library' or 'require' calls to packages already attached by Depends:
  ‘tcltk’ ‘tkrplot’
  Please remove these calls from your code.
mainNetFunction: no visible global function definition for ‘png’
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’
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 png rnorm rpois
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘LowRankQP’ ‘rgenoud’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
fn.V: no visible global function definition for ‘LowRankQP’
gaps.plot: no visible global function definition for ‘abline’
path.plot: no visible global function definition for ‘lines’
path.plot: no visible global function definition for ‘abline’
path.plot: no visible global function definition for ‘legend’
synth: no visible binding for global variable ‘sd’
synth: no visible binding for global variable ‘var’
synth: no visible global function definition for ‘LowRankQP’
Undefined global functions or variables:
  LowRankQP abline legend lines sd var
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "sd", "var")
to your NAMESPACE file.
Found the following files/directories:
  ‘test.csv’
.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.
Found the following files/directories:
  ‘.xls’ ‘attenu.xls’ ‘chick1.xls’ ‘chick2.xls’ ‘generic1.xls’
  ‘hands.xls’ ‘table1.xls’
Found the following files/directories:
  ‘myhtmlcode.html’
'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.
Package suggested but not available for checking: ‘pmatch’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tanaka.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘spruce.taper.pars.rdata’
'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.
Package suggested but not available for checking: ‘tashudata’
Running ‘testthat.R’ [21s/33s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(taxa)
  
  Attaching package: 'taxa'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  > 
  > test_check("taxa")
  ── 1. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers
  test_obj$data$my_data$taxon_id not equal to c("j", "i").
  names for target but not for current
  
  ── 2. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers
  test_obj$data$my_data$taxon_id not equal to c("j", "i").
  names for target but not for current
  
  ── 3. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers
  test_obj$data$my_data$taxon_id not equal to c("j", "i").
  names for target but not for current
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 607 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers.R#52) 
  2. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers.R#56) 
  3. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers.R#60) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘test-all.R’ [3s/15s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library("taxize")
  > test_check("taxize")
  taxize options
    taxon_state_messages: TRUE
  ── 1. Failure: fails well (@test-tol_resolve.R#56)  ────────────────────────────
  `tol_resolve(context_name = "stuff")` threw an error with unexpected message.
  Expected match: "is not valid"
  Actual message: "Timeout was reached: [api.opentreeoflife.org] Connection timed out after 10001 milliseconds"
  Backtrace:
    1. testthat::expect_error(tol_resolve(context_name = "stuff"), "is not valid")
    6. taxize::tol_resolve(context_name = "stuff")
    7. rotl::tnrs_match_names(...)
   10. rotl::tnrs_contexts(...)
   11. rotl:::.tnrs_contexts(...)
   12. rotl:::otl_POST("tnrs/contexts", body = list(), ...)
   13. httr::POST(...)
   14. httr:::request_perform(req, hu$handle$handle)
   16. httr:::request_fetch.write_memory(req$output, req$url, handle)
   17. curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 52 | SKIPPED: 207 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: fails well (@test-tol_resolve.R#56) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following files/directories:
  ‘nameNode.sqlite’
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’
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 quantile rnorm text var
Consider adding
  importFrom("graphics", "par", "text")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "optim",
             "quantile", "rnorm", "var")
  importFrom("utils", "data")
to your NAMESPACE file.
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.
CalcCorners: no visible global function definition for ‘abline’
ConvDiffCoef: no visible global function definition for ‘pascal’
ConvolveTrace: no visible global function definition for ‘filter’
DeconTrace: no visible global function definition for ‘as.Zpg’
DeconTrace: no visible global function definition for ‘butter’
DeconTrace: no visible global function definition for ‘filter’
GetDPZ: no visible global function definition for ‘data’
MakeDPZ: no visible global function definition for ‘bilinear’
MakeDPZ: no visible global function definition for ‘fft’
MakeDPZ: no visible global function definition for ‘lines’
MakeDPZ: no visible global function definition for ‘legend’
MatchCoefDPZ : CalcMisfit: no visible global function definition for
  ‘fft’
MatchCoefDPZ : CalcMisfit: no visible global function definition for
  ‘filter’
MatchCoefDPZ : generate: no visible global function definition for
  ‘runif’
MatchCoefDPZ : generate: no visible global function definition for
  ‘rnorm’
MatchCoefDPZ: no visible global function definition for ‘fft’
MatchCoefDPZ: no visible global function definition for ‘filter’
MatchCoefDPZ: no visible global function definition for ‘Zpg’
MatchCoefDPZ: no visible global function definition for ‘lines’
MatchCoefDPZ: no visible global function definition for ‘abline’
Metropolis: no visible global function definition for ‘runif’
PZ2Coef: no visible global function definition for ‘Poly’
PlotResp: no visible global function definition for ‘fft’
PlotResp: no visible global function definition for ‘filter’
PlotResp: no visible global function definition for ‘lines’
Undefined global functions or variables:
  Poly Zpg abline as.Zpg bilinear butter data fft filter legend lines
  pascal rnorm runif
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "fft", "filter", "rnorm", "runif")
  importFrom("utils", "data")
to your NAMESPACE file.
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.
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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/terra.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘ExtinctionRateChanges.txt’ ‘ExtinctionRates.txt’
  ‘MassExtinctionTimes.txt’ ‘SpeciationRateChanges.txt’
  ‘SpeciationRates.txt’ ‘SurvivalProbabilities.txt’ ‘analysis_conifer’
  ‘input_tree.tre’ ‘run_1’ ‘run_2’ ‘samples_numCategories.txt’
Package suggested but not available for checking: ‘Zelig’

Package which this enhances but not available for checking: ‘xergm’
phyper_right: no visible global function definition for ‘dhyper’
progression: no visible global function definition for ‘density’
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 ‘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 points text title
Consider adding
  importFrom("graphics", "Axis", "arrows", "legend", "points", "text",
             "title")
  importFrom("stats", "density", "dhyper", "phyper")
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 files/directories:
  ‘tmp.test.data.csv’
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.
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 ‘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 rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "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 examples in ‘tidymv-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_difference
> ### Title: Plot difference smooth from a GAM.
> ### Aliases: plot_difference
> 
> ### ** Examples
> 
> library(mgcv)
Loading required package: nlme
This is mgcv 1.8-31. For overview type 'help("mgcv-package")'.
> set.seed(10)
> data <- gamSim(4)
Factor `by' variable example
> model <- gam(y ~ fac + s(x2) + s(x2, by = fac) + s(x0), data = data)
> 
> plot_difference(model, x2, list(fac = c("1", "2")))
Error in table(predictors$Terms) - table(predictors[predictors$Label %in%  : 
  non-conformable arrays
Calls: plot_difference -> %>% -> eval -> eval
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘plot-smooths.Rmd’ using rmarkdown
Quitting from lines 172-177 (plot-smooths.Rmd) 
Error: processing vignette 'plot-smooths.Rmd' failed with diagnostics:
non-conformable arrays
--- failed re-building ‘plot-smooths.Rmd’

--- re-building ‘predict-gam.Rmd’ using rmarkdown
--- finished re-building ‘predict-gam.Rmd’

SUMMARY: processing the following file failed:
  ‘plot-smooths.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [13s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidytext)
  > 
  > test_check("tidytext")
  ── 1. Failure: Can tidy corpus from tm package (@test-corpus-tidiers.R#15)  ────
  paste(as.character(ovid[[1]]), collapse = " ") not equal to td$text[1].
  names for current but not for target
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 297 | SKIPPED: 1 | WARNINGS: 2 | FAILED: 1 ]
  1. Failure: Can tidy corpus from tm package (@test-corpus-tidiers.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
'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
'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
'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.
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.
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 ‘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 segments text write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "segments", "text")
  importFrom("stats", "aggregate", "cor", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘_paramEst.txt’
Non-standard files/directories found at top level:
  ‘DESCRIPTION.orig’ ‘README.rst’
tipom.car: no visible global function definition for ‘abline’
tipom.car: no visible global function definition for ‘axis’
tipom.heat: no visible global function definition for ‘image’
tipom.heat: no visible global function definition for ‘gray’
tipom.lw: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis gray image
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "image")
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.
Found an obsolete/platform-specific call in the following function:
  ‘.my.tkdev’
Found the platform-specific device:
  ‘X11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
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.
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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tolBasis.Rcheck/00install.out’ for details.
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.
Package suggested but not available for checking: ‘CollessLike’
Unknown package ‘CollessLike’ in Rd xrefs
Found the following files/directories:
  ‘test-001.png’ ‘test-002.png’ ‘test-003.png’ ‘test-004.png’
  ‘test-005.png’ ‘test-006.png’ ‘test-007.png’ ‘test-008.png’
  ‘test-009.png’ ‘test-010.png’ ‘test-011.png’ ‘test-012.png’
  ‘test-013.png’ ‘test-014.png’ ‘test-015.png’ ‘test-016.png’
  ‘test-017.png’ ‘test-018.png’ ‘test-019.png’ ‘test-020.png’
  ‘test-021.png’ ‘test-022.png’ ‘test-023.png’ ‘test-024.png’
  ‘test-025.png’ ‘test-026.png’ ‘test-027.png’ ‘test-028.png’
  ‘test-029.png’ ‘test-030.png’ ‘test-031.png’ ‘test-032.png’
  ‘test-033.png’ ‘test-034.png’ ‘test-035.png’ ‘test-036.png’
  ‘test-037.png’ ‘test-038.png’ ‘test-039.png’ ‘test-040.png’
  ‘test-041.png’ ‘test-042.png’ ‘test-043.png’ ‘test-044.png’
  ‘test-045.png’ ‘test-046.png’ ‘test-047.png’ ‘test-048.png’
  ‘test-049.png’ ‘test-050.png’ ‘test.pdf’
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 ‘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
  points qf qnorm rect text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axTicks", "axis", "legend", "lines",
             "par", "points", "rect", "text")
  importFrom("stats", "chisq.test", "lm", "nlm", "pbinom", "qf", "qnorm")
to your NAMESPACE file.
Found the following files/directories:
  ‘01_spontaneous lethality.txt’ ‘02.sample size.txt’
  ‘03.dosestrategy.txt’ ‘doseD4.txt’ ‘setD.txt’ ‘spoDa.txt’ ‘spoDb.txt’
align1d : obj: no visible global function definition for ‘dist’
align2d : obj: no visible global function definition for ‘dist’
align2d : pen: no visible global function definition for ‘dist’
align2d: no visible global function definition for ‘dist’
sumt: no visible global function definition for ‘optim’
tpe1d: no visible global function definition for ‘hclust’
tpe2d: no visible global function definition for ‘hclust’
tpe2d: no visible global function definition for ‘cmdscale’
Undefined global functions or variables:
  cmdscale dist hclust optim
Consider adding
  importFrom("stats", "cmdscale", "dist", "hclust", "optim")
to your NAMESPACE file.
File ‘tpr/libs/tpr.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following calls to attach():
File ‘track/R/track.attach.R’:
  attach(what = NULL, pos = pos, name = name)
See section ‘Good practice’ in ‘?attach’.
Package suggested but not available for checking: ‘taxidata’
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 ‘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 read.table uniroot write.table
Consider adding
  importFrom("graphics", "lines")
  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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘trimr-vignette.Rmd’
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 ‘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 qtnorm quantile rug
  title write.table
Consider adding
  importFrom("graphics", "lines", "mtext", "par", "rug", "title")
  importFrom("stats", "binomial", "formula", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘GTFS-table-relationships.Rmd’
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 ‘abline’
Undefined global functions or variables:
  abline approxfun head knots median optim par plot.stepfun runif
Consider adding
  importFrom("graphics", "abline", "par")
  importFrom("stats", "approxfun", "knots", "median", "optim",
             "plot.stepfun", "runif")
  importFrom("utils", "head")
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.
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’
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
  quantile rgamma rnorm runif terms
Consider adding
  importFrom("graphics", "par")
  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.
Found the following files/directories:
  ‘XMIwords.txt’
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.
.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.
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.
Found the following files/directories:
  ‘debug.txt’
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 ‘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 rbinom setTxtProgressBar
  txtProgressBar uniroot
Consider adding
  importFrom("grDevices", "gray", "palette")
  importFrom("graphics", "abline", "lines")
  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.
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.
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.
Package suggested but not available for checking: ‘USAboundariesData’
readSEER: no visible global function definition for ‘read.fwf’
Undefined global functions or variables:
  read.fwf
Consider adding
  importFrom("utils", "read.fwf")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘UScensus2000cdp/R/zzz.R’:
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000cdp\").\n")
    cat("Type help(package=\"UScensus2000cdp\") to get started.\n")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘UScensus2000tract/R/zzz.R’:
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000tract\").\n")
    cat("Type help(package=\"UScensus2000tract\") to get started.\n")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.
Found the following hidden files and directories:
  data/.Rhistory
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘rgdal’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘foreign’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘ushr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summarize_model
> ### Title: Summarize model output
> ### Aliases: summarize_model
> 
> ### ** Examples
> 
> 
> set.seed(1234567)
> 
> simulated_data <- simulate_data(nsubjects = 20)
Joining, by = "id"
> 
> model_output <- ushr(data = simulated_data)
Warning in sqrt(diag(fisher_info)) : NaNs produced
Warning in sqrt(diag(fisher_info)) : NaNs produced
Warning in sqrt(diag(fisher_info)) : NaNs produced
Warning in sqrt(diag(fisher_info)) : NaNs produced
> 
> summarize_model(model_output, data = simulated_data)
Joining, by = c("id", "Model")
Joining, by = "id"
Error: Assigned data `values` must be compatible with existing data.
ℹ Error occurred for column `ShortLifespan`.
✖ No common type for `value` <character> and `x` <double>.
Backtrace:
     █
  1. └─ushr::summarize_model(model_output, data = simulated_data)
  2.   └─`%>%`(...)
  3.     ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  4.     └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  5.       └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  6.         └─ushr:::`_fseq`(`_lhs`)
  7.           └─magrittr::freduce(value, `_function_list`)
  8.             ├─base::withVisible(function_list[[k]](value))
  9.             └─function_list[[k]](value)
 10.               └─base::replace(., is.na(.), "")
 11.                 ├─base::`[<-`(`*tmp*`, list, value = "")
 12.                 └─tibble:::`[<-.tbl_df`(`*tmp*`, list, value = "")
 13.                   └─tibble:::tbl_subassign_matrix(x, j, value, j_arg, substitute(va
Execution halted
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.
Found the following files/directories:
  ‘PredValidationPlots.pdf’ ‘RepStructValidationPlots.pdf’
Package vignette with placeholder title ‘Vignette Title’:
  ‘intro-to-varbundle.Rmd’
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 ‘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 pt qnorm quantile rnorm runif
Consider adding
  importFrom("graphics", "abline", "par")
  importFrom("stats", "ar.burg", "pchisq", "pf", "pt", "qnorm",
             "quantile", "rnorm", "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘Output.txt’ ‘Overlap.csv’ ‘Polar coordinates.csv’
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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘VBTree_vignette.Rmd’
Package suggested but not available for checking: ‘ggtern’
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 ‘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 ‘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 ‘abline’
Vdgraph: no visible global function definition for ‘par’
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 runif text
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "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.
'library' or 'require' call to ‘stats’ which was already attached by Depends.
  Please remove these calls from your code.
H: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = H, func.arg = list(func.arg), boot.arg)):
  partial argument match of ‘arg’ to ‘args’
M.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = M.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
Rel.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = Rel.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
bootstrap: warning in do.call(what = func, arg = list(boots[, , i])):
  partial argument match of ‘arg’ to ‘args’
bootstrap: warning in do.call(what = func, arg = c(abundances =
  list(boots[, , i]), func.arg)): partial argument match of ‘arg’ to
  ‘args’
d: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = d, func.arg = list(func.arg), boot.arg)):
  partial argument match of ‘arg’ to ‘args’
sim.groups: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of ‘arg’ to ‘args’
sim.table: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of ‘arg’ to ‘args’
similarity: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = similarity, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
turnover: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = turnover, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
Found the following files/directories:
  ‘Fig3-1_triple_labels_sub_and_superscripts.tiff’
  ‘Fig3-2_Euler_3set_simple_with_subscripts.tiff’
  ‘Pairwise_Venn_diagram.tiff’ ‘Quad_Venn_diagram.tiff’
  ‘Quintuple_Venn_diagram.tiff’ ‘Single_Venn_diagram.tiff’
  ‘Triple_Venn_diagram.tiff’ ‘Venn_2set_complex.tiff’
  ‘Venn_4set_pretty.tiff’ ‘Venn_5set_pretty.tiff’
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.
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.
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.
Missing or unexported object: ‘jsonlite::rbind.pages’
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 ‘lines’
Sliding.Window: no visible global function definition for ‘legend’
Undefined global functions or variables:
  axis barplot legend lines
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines")
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 ‘misc3d’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.vscc: no visible global function definition for ‘rainbow’
plot.vscc: no visible global function definition for ‘pairs’
Undefined global functions or variables:
  pairs rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "pairs")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘vwr-Ex.R’
Packages in Depends field not imported from:
  ‘lattice’ ‘latticeExtra’ ‘stringdist’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ald: no visible global function definition for ‘detectCores’
ald: no visible global function definition for ‘mclapply’
coltheart.N: no visible global function definition for ‘detectCores’
coltheart.N: no visible global function definition for ‘mclapply’
hamming.distance: no visible global function definition for
  ‘stringdist’
ldknn: no visible global function definition for ‘detectCores’
ldknn: no visible global function definition for ‘mclapply’
ldknn.odds: no visible global function definition for ‘glm’
ldknn.odds: no visible binding for global variable ‘binomial’
ldknn.odds: no visible global function definition for ‘coefficients’
levenshtein.damerau.distance: no visible global function definition for
  ‘stringdist’
levenshtein.distance: no visible global function definition for
  ‘stringdist’
plot.ldknn.run: no visible global function definition for ‘histogram’
plot.ldknn.run: no visible global function definition for
  ‘theEconomist.theme’
plot.ldknn.run: no visible global function definition for ‘xyplot’
plot.ldknn.run: no visible global function definition for ‘as.layer’
Undefined global functions or variables:
  as.layer binomial coefficients detectCores glm histogram mclapply
  stringdist theEconomist.theme xyplot
Consider adding
  importFrom("stats", "binomial", "coefficients", "glm")
to your NAMESPACE file.
Package in Depends field not imported from: ‘Rcpp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
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.
Found the following files/directories:
  ‘linout.csv’ ‘linout.pdf’ ‘out.csv’ ‘out.pdf’ ‘tabel_out.csv’
Found the following files/directories:
  ‘weisseritz’
Foreign function call to a different package:
  .C("comwr", ..., PACKAGE = "wavethresh")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘ReconstructedData.txt’ ‘ReconstructedDataStDev.txt’
  ‘ResampledReconstructions.txt’
  ‘ResampledReconstructionsStandardVariation.txt’
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.
Missing link or links in documentation object 'wdpa_clean.Rd':
  ‘[lwgeom]{st_make_valid}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
Running examples in ‘wdpar-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: st_erase_overlaps
> ### Title: Erase overlaps
> ### Aliases: st_erase_overlaps
> 
> ### ** Examples
> 
> # create data
> pl1 <- sf::st_polygon(list(matrix(c(0, 0, 2, 0, 1, 1, 0, 0), byrow = TRUE,
+                                   ncol = 2))) * 100
> pl2 <- sf::st_polygon(list(matrix(c(0, 0.5, 2, 0.5, 1, 1.5, 0, 0.5),
+                                   byrow = TRUE, ncol = 2))) * 100
> pl3 <- sf::st_polygon(list(matrix(c(0, 1.25, 2, 1.25, 1, 2.5, 0, 1.25),
+                                   byrow = TRUE, ncol = 2))) * 100
> x <- sf::st_sf(order = c("A", "B", "C"),
+                geometry = sf::st_sfc(list(pl1, pl2, pl3), crs = 3395))
> 
> # erase overlaps
> y <- st_erase_overlaps(x)
Error: 'st_make_valid' is not an exported object from 'namespace:lwgeom'
Execution halted
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # load packages
  > library(testthat)
  > library(wdpar)
  Loading required package: sf
  Linking to GEOS 3.8.1, GDAL 3.0.4, PROJ 7.0.0
  > 
  > # enable parallel testing
  > Sys.unsetenv("R_TESTS")
  > 
  > # run tests
  > test_check("wdpar")
  ── 1. Error: st_erase_overlaps (sf)  ───────────────────────────────────────────
  'st_make_valid' is not an exported object from 'namespace:lwgeom'
  Backtrace:
   1. wdpar::st_erase_overlaps(x)
   7. lwgeom::st_make_valid
   8. base::getExportedValue(pkg, name)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 9 | SKIPPED: 14 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: st_erase_overlaps (sf) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘rgeolocate’
Package vignette with placeholder title ‘Vignette Title’:
  ‘weco-vignette.Rmd’
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.
Bundesliga.Mannschaft: no visible global function definition for ‘data’
Bundesliga.Mannschaft: no visible binding for global variable
  ‘Bundesliga’
Bundesliga.Tabelle: no visible global function definition for ‘data’
Bundesliga.Tabelle: no visible binding for global variable ‘Bundesliga’
Bundesliga.XML: no visible global function definition for ‘data’
Bundesliga.XML: no visible binding for global variable ‘Bundesliga’
sens.spec: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘wikibooks/R/Bundesliga.Mannschaft.R’:
  data(Bundesliga)
File ‘wikibooks/R/Bundesliga.Tabelle.R’:
  data(Bundesliga)
File ‘wikibooks/R/Bundesliga.XML.R’:
  data(Bundesliga)
See section ‘Good practice’ in ‘?data’.
Found the following files/directories:
  ‘Bundesliga.xml’ ‘myfile.xml’
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.
Package vignette with placeholder title ‘Vignette Title’:
  ‘WindCurves_Info.Rmd’
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 points quantile sd var
Consider adding
  importFrom("graphics", "abline", "hist", "legend", "points")
  importFrom("stats", "dist", "quantile", "sd", "var")
to your NAMESPACE file.
Codoc mismatches from documentation object 'devices':
with_svg
  Code: function(new, code, width = 7, height = 7, pointsize = 12,
                 onefile = FALSE, family = "sans", bg = "white",
                 antialias = c("default", "none", "gray", "subpixel"),
                 symbolfamily)
  Docs: function(new, code, width = 7, height = 7, pointsize = 12,
                 onefile = FALSE, family = "sans", bg = "white",
                 antialias = c("default", "none", "gray", "subpixel"))
  Argument names in code not in docs:
    symbolfamily
local_svg
  Code: function(new, width = 7, height = 7, pointsize = 12, onefile =
                 FALSE, family = "sans", bg = "white", antialias =
                 c("default", "none", "gray", "subpixel"),
                 symbolfamily, .local_envir = parent.frame())
  Docs: function(new, width = 7, height = 7, pointsize = 12, onefile =
                 FALSE, family = "sans", bg = "white", antialias =
                 c("default", "none", "gray", "subpixel"), .local_envir
                 = parent.frame())
  Argument names in code not in docs:
    symbolfamily
  Mismatches in argument names:
    Position: 9 Code: symbolfamily Docs: .local_envir
Found the following files/directories:
  ‘foo’
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’
Undefined global functions or variables:
  lm par
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "lm")
to your NAMESPACE file.
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
Found the following files/directories:
  ‘aphiainfo.csv’ ‘tax.csv’
Package unavailable to check Rd xrefs: ‘cleaver’
simul.wsvm: no visible binding for global variable ‘mixture.example’
Undefined global functions or variables:
  mixture.example
Package vignette with placeholder title ‘Vignette Title’:
  ‘wTOvignette.Rmd’
File
  inst/LICENCE
will install at top-level and is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘CONTENTS’
Running ‘testthat.R’ [37s/37s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > library("wyz.code.metaTesting")
  > test_check("wyz.code.metaTesting")
  ── 1. Failure: computeArgumentsCombination (@test_computeArgumentsCombination.R#
  `d` not equal to ex[3].
  1/1 mismatches
  [1] 3 - 2 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 490 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: computeArgumentsCombination (@test_computeArgumentsCombination.R#47) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following files/directories:
  ‘Rout.a1’ ‘Rout.b1’ ‘Rout.d10’ ‘Rout.d11’ ‘Rout.d12’ ‘Rout.dat’
  ‘Rout.ftr’ ‘Rout.html’ ‘Rout.spc’ ‘Rout_Profiler.txt’ ‘Rout_err.html’
  ‘Rout_log.html’ ‘gra_Rout’
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/x13binary.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘RP2_data_1.txt’ ‘RP2_data_4.txt’ ‘RP2_qtl_1.txt’ ‘RP2_qtl_4.txt’
  ‘hp1_effect_qtl.txt’ ‘hp1_freq_mrk.txt’ ‘hp1_freq_qtl.txt’
  ‘hp1_genome.txt’ ‘hp1_last_hp_data.txt’ ‘hp1_lm_mrk.txt’
  ‘hp1_lm_qtl.txt’ ‘hp1_lm_qtl_mrk.txt’ ‘hp1_mrk.txt’ ‘hp1_qtl.txt’
  ‘hp2_effect_qtl.txt’ ‘hp2_freq_mrk.txt’ ‘hp2_freq_qtl.txt’
  ‘hp2_genome.txt’ ‘hp2_last_hp_data.txt’ ‘hp2_lm_mrk.txt’
  ‘hp2_lm_qtl.txt’ ‘hp2_lm_qtl_mrk.txt’ ‘hp2_mrk.txt’ ‘hp2_qtl.txt’
  ‘my_RP_data_1.txt’ ‘my_RP_data_4.txt’ ‘my_RP_mrk_1.txt’
  ‘my_RP_mrk_4.txt’
Found the following files/directories:
  ‘xgb.txt’
quadplot: no visible global function definition for ‘median’
xgobi: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  median write.table
Consider adding
  importFrom("stats", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
XHWE: no visible global function definition for ‘read.table’
result: no visible global function definition for ‘pchisq’
result: no visible global function definition for ‘rbinom’
result: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  pchisq rbinom read.table rmultinom
Consider adding
  importFrom("stats", "pchisq", "rbinom", "rmultinom")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘results.txt’
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.
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.
Found the following files/directories:
  ‘ggm.fit.net.pdf’
Found the following significant warnings:
  Warning: replacing previous import ‘lubridate::intersect’ by ‘raster::intersect’ when loading ‘xROI’
  Warning: replacing previous import ‘lubridate::union’ by ‘raster::union’ when loading ‘xROI’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/xROI.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘xSub_ACLED_EGY_adm0_year.csv’
Found the following files/directories:
  ‘xtable.html’ ‘xtable.tex’
Found the following files/directories:
  ‘OPT.csv’ ‘testTecan_defaultLiquid.csv’ ‘testTecan_setLiquid.csv’
Package vignette with placeholder title ‘Vignette Title’:
  ‘xyz-vignette.Rmd’
Non-standard file/directory found at top level:
  ‘CONTRIBUTORS’
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.
Found the following files/directories:
  ‘CO2.csv’
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.
Missing or unexported object: ‘devtools::use_data’
Package vignette with placeholder title ‘Vignette Title’:
  ‘ZipRadius.Rmd’
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.
Namespaces in Imports field not imported from:
  ‘DT’ ‘shinydashboard’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.9Mb
Namespaces in Imports field not imported from:
  ‘httr’ ‘progress’
  All declared Imports should be used.
Missing or unexported object: ‘devtools::use_package’
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
File ‘abundant/libs/abundant.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘rARPACK’ ‘sparseLDA’
  All declared Imports should be used.
File ‘ACDm/libs/ACDm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
File ‘acrt/libs/acrt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    R  13.9Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
File ‘adagio/libs/adagio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinydashboard’
  All declared Imports should be used.
Missing or unexported object: ‘devtools::clean_source’
asp: no visible global function definition for ‘as.formula’
asp: no visible global function definition for ‘var’
aspm: no visible binding for global variable ‘X.Declan’
aspm: no visible binding for global variable ‘Z.Jaida’
aspm: no visible binding for global variable ‘group.vec.Handan’
aspm: no visible global function definition for ‘as.formula’
aspm: no visible global function definition for ‘glm’
aspm: no visible global function definition for ‘binomial’
aspm: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘AdaptFit/R/aspm.R’:
  assign("group.vec.Handan", group.vec, pos = 1)
  assign("X.Declan", X, pos = 1)
  assign("Z.Jaida", Z, pos = 1)
Namespace in Imports field not imported from: ‘Benchmarking’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.8Mb
    pictures   2.1Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R       1.3Mb
    data    1.3Mb
    files   1.7Mb
Namespace in Imports field not imported from: ‘filehash’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    data  20.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
File ‘AdMit/libs/AdMit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
File ‘ADMMnet/libs/ADMMnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
File ‘ahaz/libs/ahaz.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mixexp’
  All declared Imports should be used.
File ‘AhoCorasickTrie/libs/AhoCorasickTrie.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘randomNames’ ‘tidyr’
  All declared Imports should be used.
File ‘akima/libs/akima.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘taxize’
  All declared Imports should be used.
File ‘AlgDesign/libs/AlgDesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘allelic/libs/allelic.so’:
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Object: ‘newallelic.o’
File ‘allelic/libs/allelic.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘tibble’
  All declared Imports should be used.
File ‘alphabetr/libs/alphabetr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.6Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘gridExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘kernlab’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinyjs’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘magrittr’
  All declared Imports should be used.
installed size is 30.1Mb
  sub-directories of 1Mb or more:
    libs  28.7Mb
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
Running examples in ‘anchoredDistr-Ex.R’ failed
The error most likely occurred in:

> ### Name: plotMAD
> ### Title: Plot the data contained in MADproject object slots.
> ### Aliases: plotMAD plotMAD,MADproject,ANY-method
> ###   plotMAD,MADproject,character-method
> 
> ### ** Examples
> 
> data(pumping)
> plotMAD(pumping, "realizations")
Error: Assigned data `x@observations` must be compatible with existing data.
✖ Existing data has 300 rows.
✖ Assigned data has 100 rows.
ℹ Only vectors of size 1 are recycled.
Backtrace:
     █
  1. ├─anchoredDistr::plotMAD(pumping, "realizations")
  2. └─anchoredDistr::plotMAD(pumping, "realizations")
  3.   ├─base::`$<-`(...)
  4.   └─tibble:::`$<-.tbl_df`(...)
  5.     └─tibble:::tbl_subassign(...)
  6.       └─tibble:::vectbl_recycle_rhs(...)
  7.         └─base::tryCatch(...)
  8.           └─base:::tryCatchList(expr, classes, parentenv, handlers)
  9.             └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10.               └─value[[3L]](cond)
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘anchoredDistr.Rmd’ using rmarkdown
Quitting from lines 85-86 (anchoredDistr.Rmd) 
Error: processing vignette 'anchoredDistr.Rmd' failed with diagnostics:
Assigned data `x@observations` must be compatible with existing data.
✖ Existing data has 300 rows.
✖ Assigned data has 100 rows.
ℹ Only vectors of size 1 are recycled.
--- failed re-building ‘anchoredDistr.Rmd’

SUMMARY: processing the following file failed:
  ‘anchoredDistr.Rmd’

Error: Vignette re-building failed.
Execution halted
File ‘anchors/libs/anchors.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘V8’
  All declared Imports should be used.
installed size is 63.6Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs    62.0Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   2.7Mb
Namespaces in Imports field not imported from:
  ‘car’ ‘datasets’ ‘dplyr’ ‘ggplot2’ ‘plotly’ ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
Namespaces in Imports field not imported from:
  ‘curl’ ‘httr’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(aoos)
  > 
  > test_check("aoos")
  ── 1. Failure: Type inheritance (@test-S4-types.R#75)  ─────────────────────────
  inherits(Child(), "Test2") isn't true.
  
  ── 2. Failure: Type with VIRTUAL (@test-S4-types.R#111)  ───────────────────────
  names(Test(x = 2)) == "x" isn't true.
  
  ── 3. Failure: Type with VIRTUAL (@test-S4-types.R#112)  ───────────────────────
  inherits(Test(), "Type") isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 187 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Type inheritance (@test-S4-types.R#75) 
  2. Failure: Type with VIRTUAL (@test-S4-types.R#111) 
  3. Failure: Type with VIRTUAL (@test-S4-types.R#112) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [10s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(apa)
  > 
  > test_check("apa")
  ── 1. Error: Output for anova_apa: repeated-measures ANOVA (@test-anova-apa.R#13
  Assigned data `<list>` must be compatible with existing data.
  ℹ Error occurred for column `df_n`.
  ✖ No common type for `value` <character> and `x` <double>.
  Backtrace:
    1. apa::anova_apa(...)
    2. apa:::anova_apa_afex(x, effect, sph_corr, es, format, info, print)
    7. tibble:::`[<-.tbl_df`(...)
    8. tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    9. tibble:::tbl_subassign_row(xj, i, value, value_arg)
   10. base::tryCatch(...)
   11. base:::tryCatchList(expr, classes, parentenv, handlers)
   12. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   13. value[[3L]](cond)
  
  ── 2. Error: Output for anova_apa: factorial repeated-measures ANOVA (@test-anov
  Assigned data `<list>` must be compatible with existing data.
  ℹ Error occurred for column `df_n`.
  ✖ No common type for `value` <character> and `x` <double>.
  Backtrace:
    1. apa::anova_apa(...)
    2. apa:::anova_apa_afex(x, effect, sph_corr, es, format, info, print)
    7. tibble:::`[<-.tbl_df`(...)
    8. tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    9. tibble:::tbl_subassign_row(xj, i, value, value_arg)
   10. base::tryCatch(...)
   11. base:::tryCatchList(expr, classes, parentenv, handlers)
   12. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   13. value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 105 | SKIPPED: 0 | WARNINGS: 9 | FAILED: 2 ]
  1. Error: Output for anova_apa: repeated-measures ANOVA (@test-anova-apa.R#135) 
  2. Error: Output for anova_apa: factorial repeated-measures ANOVA (@test-anova-apa.R#181) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
Running ‘testthat.R’ [14s/33s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(apex)
  Loading required package: ape
  Loading required package: phangorn
  > 
  > test_check("apex")
  ── 1. Error: (unknown) (@test_export.R#8)  ─────────────────────────────────────
  subscript out of bounds
  Backtrace:
   1. apex::multidna2genind(x, mlst = TRUE, gapIsNA = TRUE)
   2. adegenet::df2genind(xdfnum, ploidy = 1, ind.names = x@labels)
   3. base::vapply(...)
   4. adegenet:::FUN(X[[i]], ...)
   5. base::rowSums(out[, i, drop = FALSE], na.rm = TRUE)
   6. base::is.data.frame(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 1 ]
  1. Error: (unknown) (@test_export.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘apex.Rmd’ using rmarkdown
Quitting from lines 294-299 (apex.Rmd) 
Error: processing vignette 'apex.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘apex.Rmd’

SUMMARY: processing the following file failed:
  ‘apex.Rmd’

Error: Vignette re-building failed.
Execution halted
File ‘APIS/libs/APIS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
File ‘apple/libs/apple.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
runAPSIM: warning in scan(reports_file[i], "", sep = "", skip =
  length(temp), nline = 1): partial argument match of 'nline' to
  'nlines'
runAPSIM: no visible global function definition for ‘write.table’
runAPSIM: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  am.c:275:9: warning: comparison of array 'readByte' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/aqr.Rcheck/00install.out’ for details.
File ‘aqr/libs/aqr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘purrr’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R             2.3Mb
    help          1.1Mb
    testScripts   1.3Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘gmm’ ‘graphics’ ‘sandwich’ ‘stats4’ ‘utils’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.6Mb
File ‘ash/libs/ash.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘arules’ ‘arulesViz’ ‘dplyr’ ‘methods’ ‘plotly’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
File ‘AssotesteR/libs/AssotesteR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   9.6Mb
File ‘audio/libs/audio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘broom’ ‘diptest’ ‘ggplot2’ ‘hexbin’ ‘moments’
  All declared Imports should be used.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R.utils’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    java   7.8Mb
installed size is 67.2Mb
  sub-directories of 1Mb or more:
    java  67.2Mb
Namespace in Imports field not imported from: ‘openssl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘jose’ ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
File ‘BaBooN/libs/BaBooN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is 93.7Mb
  sub-directories of 1Mb or more:
    libs  92.5Mb
Package suggested but not available for checking: ‘mzR’
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
File ‘BALD/libs/BALD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘docopt’
  All declared Imports should be used.
Running examples in ‘BANEScarparkinglite-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_range_crude
> ### Title: Download records from a specified range from the Bath: Hacked
> ###   datastore
> ### Aliases: get_range_crude
> 
> ### ** Examples
> 
> # Records for 1st June 2016
> raw_data <- get_range_crude("2016-06-01 00:00:00", "2016-06-01 23:59:59")
Making request to Socrata Open Data API...
Error in open.connection(con, "rb") : HTTP error 404.
Calls: get_range_crude ... datasource_connection -> read_connection -> open -> open.connection
Execution halted
Namespace in Imports field not imported from: ‘ranger’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
File ‘Barnard/libs/Barnard.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    libs  27.0Mb
Namespace in Imports field not imported from: ‘mvnfast’
  All declared Imports should be used.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.1Mb
    libs   5.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   3.2Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
File ‘base64enc/libs/base64enc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 78.3Mb
  sub-directories of 1Mb or more:
    libs  76.3Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Found the following significant warnings:
  rcpparma_hello_world.cpp:930:4: warning: explicitly assigning value of variable of type 'arma::colvec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
  rcpparma_hello_world.cpp:930:12: warning: explicitly assigning value of variable of type 'arma::colvec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
  rcpparma_hello_world.cpp:939:4: warning: explicitly assigning value of variable of type 'arma::colvec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
  rcpparma_hello_world.cpp:939:12: warning: explicitly assigning value of variable of type 'arma::colvec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/BayesBD.Rcheck/00install.out’ for details.
File ‘BayesComm/libs/BayesComm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘msm’
  All declared Imports should be used.
installed size is 73.1Mb
  sub-directories of 1Mb or more:
    libs  72.2Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MatrixModels’
  All declared Imports should be used.
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  16.0Mb
File ‘bayesGARCH/libs/bayesGARCH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘shinytest’ ‘testthat’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.9Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
File ‘bayesloglin/libs/bayesloglin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Namespace in Imports field not imported from: ‘FastGP’
  All declared Imports should be used.
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs  30.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   4.1Mb
File ‘bayesQR/libs/bayesQR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs  15.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    ex-data   4.7Mb
File ‘BayesTree/libs/BayesTree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 133.8Mb
  sub-directories of 1Mb or more:
    libs  133.7Mb
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘matrixStats’ ‘reshape2’ ‘scales’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘locfit’ ‘secr’
  All declared Imports should be used.
File ‘BCBCSF/libs/BCBCSF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘coda’ ‘knitr’ ‘plyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
File ‘Bclim/libs/Bclim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  sparseFactor.cpp:33:10: warning: explicitly assigning value of variable of type 'Rcpp::IntegerVector' (aka 'Vector<13>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/BClustLonG.Rcheck/00install.out’ for details.
File ‘bcpa/libs/bcpa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rlang’
  All declared Imports should be used.
File ‘bcv/libs/bcv.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 108.9Mb
  sub-directories of 1Mb or more:
    libs  107.4Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘chron’ ‘colorspace’ ‘gtable’ ‘htmltools’ ‘htmlwidgets’
  ‘httpuv’ ‘magrittr’ ‘munsell’ ‘plyr’ ‘scales’ ‘stringi’ ‘xtable’
  ‘yaml’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘png’
  All declared Imports should be used.
File ‘BenfordTests/libs/BenfordTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 28.1Mb
  sub-directories of 1Mb or more:
    libs  27.0Mb
Namespace in Imports field not imported from: ‘BiDAG’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘compiler’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘ggplot2’ ‘readxl’ ‘rlist’ ‘shinyBS’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
File ‘betategarch/libs/betategarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Note: found 4 marked Latin-1 strings
  Note: found 611 marked UTF-8 strings
installed size is 135.0Mb
  sub-directories of 1Mb or more:
    include  134.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
File ‘BiasedUrn/libs/BiasedUrn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    1.9Mb
Namespace in Imports field not imported from: ‘nycflights13’
  All declared Imports should be used.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  11.1Mb
possible bashism in configure line 12 (echo -n):
  echo -n "  checking for Sun Studio compiler..."
  possible bashism in configure line 22 (echo -n):
  echo -n "  checking for OS..."
File ‘biganalytics/libs/biganalytics.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
File ‘bigGP/libs/bigGP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
File ‘biglm/libs/biglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   2.5Mb
    libs      2.4Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
possible bashism in configure line 14 (echo -n):
  echo -n "  checking for Sun Studio compiler..."
  possible bashism in configure line 24 (echo -n):
  echo -n "  checking for OS..."
File ‘bigReg/libs/bigReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs     12.3Mb
possible bashism in configure line 13 (echo -n):
  echo -n "  checking for Sun Studio compiler..."
  possible bashism in configure line 23 (echo -n):
  echo -n "  checking for OS..."
File ‘bigtabulate/libs/bigtabulate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘lattice’ ‘zoo’
  All declared Imports should be used.
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  17.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
File ‘bild/libs/bild.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.4Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
File ‘binom/libs/binom.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
Package suggested but not available for checking: ‘msa’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Package suggested but not available for checking: ‘BiocVersion’
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/Biograph.Rcheck/00install.out’ for details.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   8.7Mb
Namespace in Imports field not imported from: ‘fs’
  All declared Imports should be used.
File ‘bioPN/libs/bioPN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    doc       1.3Mb
    extdata   1.7Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
Namespaces in Imports field not imported from:
  ‘esquisse’ ‘rgdal’
  All declared Imports should be used.
Running examples in ‘biscale-Ex.R’ failed
The error most likely occurred in:

> ### Name: bi_class
> ### Title: Create Classes for Bivariate Maps
> ### Aliases: bi_class
> 
> ### ** Examples
> 
> # quantile breaks, 2x2
> data <- bi_class(stl_race_income, x = pctWhite, y = medInc, style = "quantile", dim = 2)
Warning in bi_class(stl_race_income, x = pctWhite, y = medInc, style = "quantile",  :
  The 'sf' package is not loaded, and the class 'sf' attribute of the given data set has been lost. Load 'sf' to retain the class when using 'bi_class'.
Error: All columns in a tibble must be vectors.
✖ Column `geometry` is a `sfc_POLYGON/sfc` object.
Backtrace:
     █
  1. └─biscale::bi_class(...)
  2.   ├─dplyr::mutate(.data, bi_x = cut(!!xQ, breaks = bins_x, include.lowest = TRUE))
  3.   └─dplyr:::mutate.data.frame(...)
  4.     ├─base::as.data.frame(mutate(tbl_df(.data), ...))
  5.     ├─dplyr::mutate(tbl_df(.data), ...)
  6.     └─dplyr::tbl_df(.data)
  7.       ├─tibble::as_tibble(data, .name_repair = "check_unique")
  8.       └─tibble:::as_tibble.data.frame(data, .name_repair = "check_unique")
  9.         └─tibble:::lst_to_tibble(unclass(x), .rows, .name_repair)
 10.           └─tibble:::check_valid_cols(x)
Execution halted
Running ‘testthat.R’ [5s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(biscale)
  > 
  > test_check("biscale")
  ── 1. Error: sf warning is triggered (@test_bi_class.R#10)  ────────────────────
  All columns in a tibble must be vectors.
  ✖ Column `geometry` is a `sfc_POLYGON/sfc` object.
  Backtrace:
    1. testthat::expect_warning(...)
    6. biscale::bi_class(...)
    8. dplyr:::mutate.data.frame(...)
   11. dplyr::tbl_df(.data)
   13. tibble:::as_tibble.data.frame(data, .name_repair = "check_unique")
   14. tibble:::lst_to_tibble(unclass(x), .rows, .name_repair)
   15. tibble:::check_valid_cols(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 82 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: sf warning is triggered (@test_bi_class.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
File ‘bitops/libs/bitops.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘corrgram’ ‘rpivotTable’ ‘shinyAce’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Package suggested but not available for checking: ‘RQuantLib’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RGtk2’ ‘cairoDevice’ ‘ergm’ ‘foreign’ ‘gWidgets’ ‘gWidgetsRGtk2’
  ‘haven’ ‘plot3D’ ‘plot3Drgl’ ‘rgl’ ‘sna’ ‘statnet.common’
  All declared Imports should be used.
installed size is 55.3Mb
  sub-directories of 1Mb or more:
    libs  53.4Mb
Package suggested but not available for checking: ‘bigrf’

Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’
  ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
Missing or unexported object: ‘xgboost::predict’
installed size is 60.5Mb
  sub-directories of 1Mb or more:
    libs  59.2Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
File ‘blockmodels/libs/blockmodels.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘ggplot2’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
File ‘Bmix/libs/Bmix.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 36.3Mb
  sub-directories of 1Mb or more:
    libs  35.9Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
File ‘BMRV/libs/BMRV.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘fastDummies’
  All declared Imports should be used.
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.7Mb
installed size is 371.1Mb
  sub-directories of 1Mb or more:
    include    8.8Mb
    lib      361.9Mb
installed size is 81.1Mb
  sub-directories of 1Mb or more:
    libs  80.6Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘psychTools’
  All declared Imports should be used.
File ‘bootruin/libs/bootruin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
File ‘bqtl/libs/bqtl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘CCA’ ‘brainR’ ‘elasticnet’
  All declared Imports should be used.
File ‘brainwaver/libs/brainwaver.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘connexity_small_world.o’
File ‘brainwaver/libs/brainwaver.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

> ### Name: get_brmap
> ### Title: Get Brazilian maps from different geographic levels
> ### Aliases: get_brmap
> ### Keywords: IBGE geographic levels shapefile spatial
> 
> ### ** Examples
> 
> ## Retrieving the map from the State of Rio de Janeiro
> rio_map <- get_brmap(geo = "State",
+                      geo.filter = list(State = 33),
+                      class = "sf")
Error: All columns in a tibble must be vectors.
✖ Column `geometry` is a `sfc_MULTIPOLYGON/sfc` object.
Backtrace:
     █
  1. └─brazilmaps::get_brmap(...)
  2.   └─`%>%`(...)
  3.     ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  4.     └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  5.       └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  6.         └─brazilmaps:::`_fseq`(`_lhs`)
  7.           └─magrittr::freduce(value, `_function_list`)
  8.             └─function_list[[i]](value)
  9.               ├─dplyr::filter(., brmap[[(names(geo.filter)[i])]] %in% geo.filter[[i]])
 10.               └─dplyr:::filter.data.frame(...)
 11.                 ├─base::as.data.frame(filter(tbl_df(.data), ..., .preserve = .preserve))
 12.                 ├─dplyr::filter(tbl_df(.data), ..., .preserve = .preserve)
 13.                 └─dplyr::tbl_df(.data)
 14.                   ├─tibble::as_tibble(data, .name_repair = "chec
Execution halted
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    libs  27.4Mb
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘profileModel’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R     3.5Mb
    doc   2.6Mb
Error(s) in re-building vignettes:
--- re-building ‘broom_mixed_intro.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Registered S3 methods overwritten by 'broom.mixed':
  method         from 
  augment.lme    broom
  augment.merMod broom
  glance.lme     broom
  glance.merMod  broom
  glance.stanreg broom
  tidy.brmsfit   broom
  tidy.gamlss    broom
  tidy.lme       broom
  tidy.merMod    broom
  tidy.rjags     broom
  tidy.stanfit   broom
  tidy.stanreg   broom
Loading required package: brms
Loading required package: Rcpp
Loading 'brms' package (version 2.12.0). Useful instructions
can be found by typing help('brms'). A more detailed introduction
to the package is available through vignette('brms_overview').

Attaching package: 'brms'

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

    ar

Loading required package: dotwhisker
Loading required package: ggplot2
Warning: `data_frame()` is deprecated as of tibble 1.1.0.
Please use `tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Quitting from lines 68-82 (broom_mixed_intro.rmd) 
Error: processing vignette 'broom_mixed_intro.rmd' failed with diagnostics:
Aesthetics must be either length 1 or the same as the data (6): xmin and xmax
--- failed re-building ‘broom_mixed_intro.rmd’

SUMMARY: processing the following file failed:
  ‘broom_mixed_intro.rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    bin    2.7Mb
    doc    1.1Mb
    libs   2.6Mb
Namespaces in Imports field not imported from:
  ‘rworldxtra’ ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
installed size is 42.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  40.4Mb
Namespaces in Imports field not imported from:
  ‘mvtnorm’ ‘ssmn’
  All declared Imports should be used.
installed size is 105.5Mb
  sub-directories of 1Mb or more:
    libs  104.7Mb
File ‘BTYDplus/libs/BTYDplus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘modeldata’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
File ‘bvarsv/libs/bvarsv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
File ‘bvls/libs/bvls.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
File ‘bytescircle/libs/bytescircle.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘here’ ‘withr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/Cairo.Rcheck/00install.out’ for details.
File ‘CAMAN/libs/CAMAN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.2Mb
Running ‘cX-ui-functions.R’
  Running ‘cx-get-ui-generated-test-setup.R’
  Running ‘testthat.R’ [13s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(canvasXpress)
  > 
  > #NOTE: temporary until canvasXpress.data is on CRAN
  > get_data <- function(file_name) {
  +     system.file("extdata", file_name, package = "canvasXpress")
  + }
  > 
  > 
  > test_check("canvasXpress")
  ── 1. Error: Barplot URL data (@test-other-data-url.R#5)  ──────────────────────
  Could not resolve host: www.canvasxpress.org
  Backtrace:
    1. canvasXpress::canvasXpress(...)
    2. canvasXpress:::assertDataCorrectness(data, graphType, config)
    4. httr:::http_error.character(data)
    6. httr::HEAD(x, ...)
    7. httr:::request_perform(req, hu$handle$handle)
    9. httr:::request_fetch.write_memory(req$output, req$url, handle)
   10. curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 817 | SKIPPED: 0 | WARNINGS: 30 | FAILED: 1 ]
  1. Error: Barplot URL data (@test-other-data-url.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Namespace in Imports field not imported from: ‘details’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R        1.1Mb
    data     1.5Mb
    models   2.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Namespace in Imports field not imported from: ‘g.data’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘animation’ ‘devtools’ ‘gapminder’ ‘knitr’ ‘rlist’ ‘rmarkdown’
  ‘roxygen2’ ‘sde’ ‘shiny’ ‘tidyverse’ ‘usethis’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘janitor’ ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
Found the following significant warnings:
  ../inst/include/SignificantIntervalSearchFais.h:97:17: warning: 'saveSignificantInterval' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  ../inst/include/SignificantIntervalSearchFais.h:100:17: warning: 'saveTestableInterval' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
See ‘/data/gannet/ripley/R/packages/tests-clang/CASMAP.Rcheck/00install.out’ for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘broom’ ‘epitools’
  All declared Imports should be used.
File ‘catIrt/libs/catIrt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   1.1Mb
    libs      3.1Mb
Namespace in Imports field not imported from: ‘prettydoc’
  All declared Imports should be used.
File ‘cbird/libs/cbird.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 217.4Mb
  sub-directories of 1Mb or more:
    libs  216.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
estim.regul: warning in matrix(res, nc = length(grid2)): partial
  argument match of 'nc' to 'ncol'
comput: no visible global function definition for ‘cor’
img.estim.regul: no visible global function definition for ‘par’
img.estim.regul: no visible global function definition for ‘image’
img.estim.regul: no visible global function definition for
  ‘heat.colors’
img.estim.regul: no visible global function definition for ‘axis’
img.estim.regul: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘par’
img.matcor: no visible global function definition for ‘image’
img.matcor: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘abline’
img.matcor: no visible global function definition for ‘layout’
loo: no visible global function definition for ‘cor’
matcor: no visible global function definition for ‘cor’
plt.cc: no visible global function definition for ‘par’
plt.cc: no visible global function definition for ‘layout’
plt.indiv: no visible global function definition for ‘text’
plt.indiv: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘points’
plt.var: no visible global function definition for ‘text’
plt.var: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘lines’
rcc: no visible global function definition for ‘var’
rcc: no visible global function definition for ‘cov’
Undefined global functions or variables:
  abline axis box cor cov heat.colors image layout lines par points
  text var
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "lines", "par", "points", "text")
  importFrom("stats", "cor", "cov", "var")
to your NAMESPACE file.
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs  21.9Mb
File ‘cccp/libs/cccp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   4.3Mb
File ‘CDVine/libs/CDVine.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.3Mb
File ‘cec2013/libs/cec2013.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.7Mb
    libs   7.0Mb
File ‘censNID/libs/censNID.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
File ‘cents/libs/cents.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘base’ ‘stats’ ‘tidyr’
  All declared Imports should be used.
File ‘cgAUC/libs/cgAUC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Found the following significant warnings:
  costfunctions.c:33:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  costfunctions.c:57:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/changepoint.np.Rcheck/00install.out’ for details.
File ‘changepoint/libs/changepoint.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘foreach’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
File ‘ChIPtest/libs/ChIPtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
Namespace in Imports field not imported from: ‘forcats’
  All declared Imports should be used.
File ‘CHsharp/libs/CHsharp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘stringr’
  All declared Imports should be used.
File ‘CIFsmry/libs/CIFsmry.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘circlize’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   5.7Mb
Namespaces in Imports field not imported from:
  ‘RInside’ ‘circular’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinyBS’
  All declared Imports should be used.
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
File ‘ClickClust/libs/ClickClust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘clogitL1/libs/clogitL1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [4m/22m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(clubSandwich)
  Registered S3 method overwritten by 'clubSandwich':
    method    from    
    bread.mlm sandwich
  > 
  > test_check("clubSandwich")
  ── 1. Failure: Order doesn't matter. (@test_lmerMod.R#153)  ────────────────────
  `Wald_fit` not equal to `Wald_scramble`.
  Component 19: Component 4: Mean relative difference: 1.550445e-08
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 754 | SKIPPED: 11 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Order doesn't matter. (@test_lmerMod.R#153) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘KernSmooth’
  All declared Imports should be used.
possible bashism in cleanup line 15 (brace expansion):
  rm -f src/*.{o,so,mod}
  possible bashism in cleanup line 17 (brace expansion):
  rm -f config.{log,status}
  possible bashism in cleanup line 22 (brace expansion):
  rm -f vignettes/*.{tex,aux,bbl,blg,log,toc,idx,ind,ilg,out,synctex.gz}
File ‘clustering.sc.dp/libs/clustering.sc.dp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘purrr’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
File ‘ClusterStability/libs/ClusterStability.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
File ‘ClustMMDD/libs/ClustMMDD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘datasets’ ‘dplyr’ ‘klaR’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
File ‘clv/libs/clv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘caret’ ‘e1071’ ‘epitools’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Imports includes 42 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   5.3Mb
File ‘COBRA/libs/COBRA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘nnet’
  All declared Imports should be used.
File ‘codadiags/libs/codadiags.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘graphics’ ‘jsonlite’ ‘pander’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘methods’ ‘readr’
  All declared Imports should be used.
File ‘coenoflex/libs/coenoflex.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘yaml’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘coin’ ‘ggplot2’ ‘plyr’
  All declared Imports should be used.
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  24.3Mb
Error(s) in re-building vignettes:
--- re-building ‘collateral.Rmd’ using rmarkdown
Quitting from lines 221-229 (collateral.Rmd) 
Error: processing vignette 'collateral.Rmd' failed with diagnostics:
Input must be a vector, not a `safely_mapped` object.
--- failed re-building ‘collateral.Rmd’

SUMMARY: processing the following file failed:
  ‘collateral.Rmd’

Error: Vignette re-building failed.
Execution halted
File ‘collUtils/libs/collUtils.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    extdata   2.1Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
Package suggested but not available for checking: ‘CAM’

Suggests orphaned package: ‘flare’
File ‘compareC/libs/compareC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘stringr’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   2.3Mb
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  27.0Mb
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    libs  22.9Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘checkmate’ ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  All declared Imports should be used.
Running examples in ‘concaveman-Ex.R’ failed
The error most likely occurred in:

> ### Name: concaveman
> ### Title: concaveman: A very fast 2D concave hull algorithm.
> ### Aliases: concaveman concaveman-package concaveman concaveman.matrix
> ###   concaveman.sf concaveman.SpatialPoints
> 
> ### ** Examples
> 
> data(points)
> polygons <- concaveman(points)
Error: All columns in a tibble must be vectors.
✖ Column `geometry` is a `sfc_POINT/sfc` object.
Backtrace:
     █
  1. ├─concaveman::concaveman(points)
  2. └─concaveman:::concaveman.sf(points)
  3.   └─`%>%`(...)
  4.     ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  5.     └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  6.       └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  7.         └─concaveman:::`_fseq`(`_lhs`)
  8.           └─magrittr::freduce(value, `_function_list`)
  9.             ├─base::withVisible(function_list[[k]](value))
 10.             └─function_list[[k]](value)
 11.               ├─dplyr::summarise(...)
 12.               └─dplyr:::summarise.data.frame(...)
 13.                 ├─base::as.data.frame(summarise(tbl_df(.data), ...))
 14.                 ├─dplyr::summarise(tbl_df(.data), ...)
 15.                 └─dplyr::tbl_df(.data)
 16.                   ├─tibble::as_tibble(d
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
File ‘ConConPiWiFun/libs/ConConPiWiFun.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘compiler’ ‘rlang’
  All declared Imports should be used.
Running examples in ‘concurve-Ex.R’ failed
The error most likely occurred in:

> ### Name: curve_corr
> ### Title: Computes Consonance Intervals for Correlations
> ### Aliases: curve_corr
> 
> ### ** Examples
> 
> 
> GroupA <- rnorm(50)
> GroupB <- rnorm(50)
> joe <- curve_corr(x = GroupA, y = GroupB, alternative = "two.sided", method = "pearson")
> tibble::tibble(joe[[1]])
Error: All columns in a tibble must be vectors.
✖ Column `joe[[1]]` is a `data.frame/concurve` object.
Backtrace:
    █
 1. └─tibble::tibble(joe[[1]])
 2.   └─tibble:::tibble_quos(xs[!is_null], .rows, .name_repair)
 3.     └─tibble:::check_valid_col(res, col_names[[j]], j)
 4.       └─tibble:::check_valid_cols(set_names(list(x), name))
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘examples.Rmd’ using rmarkdown
Quitting from lines 51-52 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
All columns in a tibble must be vectors.
✖ Column `intervalsdf[[1]]` is a `data.frame/concurve` object.
--- failed re-building ‘examples.Rmd’

--- re-building ‘stata.Rmd’ using rmarkdown
--- finished re-building ‘stata.Rmd’

SUMMARY: processing the following file failed:
  ‘examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Missing or unexported object: ‘xlsx::CellBlock.default’
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data      6.5Mb
    extdata   2.6Mb
File ‘condSURV/libs/condSURV.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘cli’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reshape’
  All declared Imports should be used.
File ‘ConsReg/libs/ConsReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 70.6Mb
  sub-directories of 1Mb or more:
    libs  69.4Mb
Namespaces in Imports field not imported from:
  ‘geosphere’ ‘igraph’ ‘methods’ ‘rgdal’ ‘sf’
  All declared Imports should be used.
File ‘contoureR/libs/contoureR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘formattable’ ‘gridExtra’ ‘kableExtra’ ‘knitr’ ‘magrittr’
  ‘readr’ ‘readxl’ ‘tidyverse’
  All declared Imports should be used.
Running examples in ‘convergEU-Ex.R’ failed
The error most likely occurred in:

> ### Name: country_ranking
> ### Title: Ranking of EU countries by time
> ### Aliases: country_ranking
> 
> ### ** Examples
> 
> 
> # Example 1
> # Sorted dataframe in the format years by countries:
> require(tibble)
Loading required package: tibble
> myTB  <- tibble::tribble(
+ ~years, ~UK, ~DE, ~IT,
+ 1988,   1201, 868, 578,
+ 1989,   1150, 978, 682,
+ 1990,   998,  1250, 332,
+ 1991,  1600,  1350, 802
+ )
> 
> # Country ranking according to the indicator higher is the best:
> res <- country_ranking(myTB,timeName="years")
Error: Assigned data `rank(unlist(ord_MS[auxMS, -posizTime]), ties.method = "min")` must be compatible with row subscript `auxMS`.
✖ 1 row must be assigned.
✖ Assigned data has 3 rows.
ℹ Only vectors of size 1 are recycled.
Backtrace:
    █
 1. └─convergEU::country_ranking(myTB, timeName = "years")
 2.   ├─base::`[<-`(...)
 3.   └─tibble:::`[<-.tbl_df`(...)
 4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 5.       └─tibble:::vectbl_recycle_rhs(...)
 6.         └─base::tryCatch(...)
 7.           └─base:::tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)
Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   5.0Mb
Namespace in Imports field not imported from: ‘mcc’
  All declared Imports should be used.
File ‘cord/libs/cord.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘rmarkdown’ ‘shinyWidgets’ ‘shinydashboard’
  ‘shinyjs’
  All declared Imports should be used.
Running examples in ‘corpus-Ex.R’ failed
The error most likely occurred in:

> ### Name: text_locate
> ### Title: Searching for Terms
> ### Aliases: text_count text_detect text_locate text_match text_sample
> ###   text_subset
> 
> ### ** Examples
> 
> text <- c("Rose is a rose is a rose is a rose.",
+           "A rose by any other name would smell as sweet.",
+           "Snow White and Rose Red")
> 
> text_count(text, "rose")
[1] 4 1 1
> text_detect(text, "rose")
[1] TRUE TRUE TRUE
> text_locate(text, "rose")
Error in sum(colwidths) : invalid 'type' (list) of argument
Calls: <Anonymous> ... print.corpus_text_locate -> format.corpus_text_locate
Execution halted
Running ‘testthat.R’ [11s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(corpus)
  > 
  > test_check("corpus")
  -- 1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161
  invalid 'type' (list) of argument
  Backtrace:
    1. base::strsplit(capture_output(print(loc), width = 76), "\n")
    9. corpus:::print.corpus_text_locate(loc)
   10. corpus:::format.corpus_text_locate(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 601 | SKIPPED: 5 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘profr’ ‘xtable’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.8Mb
Package suggested but not available for checking: ‘xcms’
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    libs  29.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    help   1.6Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   6.9Mb
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
File ‘COUSCOus/libs/COUSCOus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Namespace in Imports field not imported from: ‘gstat’
  All declared Imports should be used.
File ‘covBM/libs/covBM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘data.table’ ‘dplyr’ ‘markdown’ ‘shinyjs’ ‘table1’
  ‘tidyr’
  All declared Imports should be used.
Running ‘testthat.R’ [7s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(covid19us)
  > 
  > test_check("covid19us")
  ── 1. Failure: get_states_daily works (@test-all.R#21)  ────────────────────────
  nrow(too_early) not equal to 0.
  1/1 mismatches
  [1] 1 - 0 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 12 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: get_states_daily works (@test-all.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘misc3d’
  All declared Imports should be used.
File ‘CoxBoost/libs/CoxBoost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
Namespace in Imports field not imported from: ‘coxme’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
File ‘CoxPlus/libs/CoxPlus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘grDevices’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘cents’
  All declared Imports should be used.
File ‘cpm/libs/cpm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gWidgetsRGtk2’
  All declared Imports should be used.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
File ‘cqrReg/libs/cqrReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
Note: found 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Namespaces in Imports field not imported from:
  ‘gdistance’ ‘raster’
  All declared Imports should be used.
File ‘credule/libs/credule.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Namespace in Imports field not imported from: ‘glue’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘r6extended’
  All declared Imports should be used.
File ‘crrp/libs/crrp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  27.8Mb
Namespace in Imports field not imported from: ‘survminer’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘qte’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    shp   7.8Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data  10.9Mb
Note: found 59670 marked Latin-1 strings
  Note: found 16 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘epitools’ ‘rpivotTable’ ‘shinyMatrix’
  All declared Imports should be used.
installed size is 113.2Mb
  sub-directories of 1Mb or more:
    R       1.1Mb
    libs  110.1Mb
Namespaces in Imports field not imported from:
  ‘numDeriv’ ‘pkgbuild’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   3.6Mb
File ‘cusp/libs/cusp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lattice’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
File ‘cvxbiclustr/libs/cvxbiclustr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  'gurobi', 'Rcplex', 'rcbc'
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    doc    1.2Mb
    help   1.0Mb
    libs   5.9Mb
File ‘cycleRtools/libs/cycleRtools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
Note: found 4 marked Latin-1 strings
  Note: found 21 marked UTF-8 strings
File ‘DALY/libs/DALY.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘expm’
  All declared Imports should be used.
File ‘darts/libs/darts.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
Namespace in Imports field not imported from: ‘DatabaseConnectorJars’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   4.4Mb
Namespace in Imports field not imported from: ‘miniUI’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘shinyFiles’ ‘shinycssloaders’ ‘shinyjs’ ‘shinythemes’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
.onLoad : <anonymous>: no visible global function definition for
  ‘read.table’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbConnect’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbListTables’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbExistsTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbReadTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbWriteTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbDisconnect’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbRemoveTable’
Undefined global functions or variables:
  dbConnect dbDisconnect dbExistsTable dbListTables dbReadTable
  dbRemoveTable dbWriteTable read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
File ‘datamap/libs/datamap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘future’ ‘iterators’ ‘readr’
  All declared Imports should be used.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   5.5Mb
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Found the following significant warnings:
  WARNING: ignoring environment value of R_HOME
See ‘/data/gannet/ripley/R/packages/tests-clang/datasailr.Rcheck/00install.out’ for details.
installed size is 51.7Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  49.6Mb
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
File ‘dblcens/libs/dblcens.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘dplyr’
  All declared Imports should be used.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
File ‘DCluster/libs/DCluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘CDM’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
File ‘DDHFm/libs/DDHFm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
Note: found 1 marked Latin-1 string
  Note: found 46826 marked UTF-8 strings
File ‘decon/libs/decon.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘UScensus2010’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘UScensus2010’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘JavaGD’ ‘OpenStreetMap’ ‘maptools’ ‘rgdal’ ‘scales’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘deformula/libs/deformula.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘assertthat’
  All declared Imports should be used.
installed size is 87.3Mb
  sub-directories of 1Mb or more:
    libs  84.6Mb
File ‘delt/libs/delt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
File ‘DendSer/libs/DendSer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       4.9Mb
    extdata   2.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
File ‘depth/libs/depth.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.8Mb
    help   1.4Mb
    libs   3.4Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
File ‘desire/libs/desire.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.6Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘utils’
  All declared Imports should be used.
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   7.4Mb
File ‘dfphase1/libs/dfphase1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 53.6Mb
  sub-directories of 1Mb or more:
    libs  53.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
File ‘dgof/libs/dgof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  ../inst/include/adept/adept_source.h:560:6: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ../inst/include/adept/adept_source.h:561:6: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ../inst/include/adept/adept_source.h:616:6: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ../inst/include/adept/adept_source.h:617:6: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ../inst/include/adept/adept_source.h:1147:8: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ../inst/include/adept/adept_source.h:1148:8: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/data/gannet/ripley/R/packages/tests-clang/dgumbel.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘mgcv’
  All declared Imports should be used.
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    doc           9.7Mb
    htmlwidgets   5.9Mb
File ‘DiceOptim/libs/DiceOptim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 37 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.

Requires orphaned package: ‘clValid’
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
File ‘diffIRT/libs/diffIRT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘sf’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gplots’
  All declared Imports should be used.
File ‘diffrprojects/libs/diffrprojects.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
File ‘DiffusionRgqd/libs/DiffusionRgqd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
File ‘DiffusionRjgqd/libs/DiffusionRjgqd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Found the following significant warnings:
  Note: possible error in 'glmer(y ~ items + (1 | ': unused argument (REML = FALSE) 
See ‘/data/gannet/ripley/R/packages/tests-clang/difR.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 ‘dils/libs/dils.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘sandwich’
  All declared Imports should be used.
File ‘DIRECT/libs/DIRECT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’ ‘splancs’ ‘utils’
  All declared Imports should be used.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
File ‘dismo/libs/dismo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘proxy’
  All declared Imports should be used.
File ‘distory/libs/distory.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
File ‘dkDNA/libs/dkDNA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    include  16.7Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   2.1Mb
    libs   4.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Running examples in ‘DMwR2-Ex.R’ failed
The error most likely occurred in:

> ### Name: centralImputation
> ### Title: Fill in NA values with central statistics
> ### Aliases: centralImputation
> ### Keywords: models
> 
> ### ** Examples
> 
> data(algae,package="DMwR2")
> cleanAlgae <- centralImputation(algae)
Error: `i` must have one dimension, not 2.
Execution halted
Namespaces in Imports field not imported from:
  ‘GOstats’ ‘caTools’ ‘fdrtool’
  All declared Imports should be used.
File ‘documair/libs/documair.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  12.1Mb
Error(s) in re-building vignettes:
--- re-building ‘dodgr.Rmd’ using rmarkdown
Quitting from lines 323-330 (dodgr.Rmd) 
Error: processing vignette 'dodgr.Rmd' failed with diagnostics:
`x` must be a vector, not a `sfc_LINESTRING/sfc` object.
--- failed re-building ‘dodgr.Rmd’

--- re-building ‘times.Rmd’ using rmarkdown
--- finished re-building ‘times.Rmd’

SUMMARY: processing the following file failed:
  ‘dodgr.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘parallel’ ‘rgdal’ ‘sp’ ‘tensorflow’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
installed size is 33.6Mb
  sub-directories of 1Mb or more:
    libs  31.3Mb
Namespaces in Imports field not imported from:
  ‘bit64’ ‘rstudioapi’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespaces in Imports field not imported from:
  ‘tools’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘broom’ ‘colorspace’ ‘colourpicker’ ‘cowplot’
  ‘igraph’ ‘magrittr’ ‘shinyBS’ ‘shinyWidgets’ ‘shinydashboard’
  ‘shinythemes’ ‘tidyverse’ ‘visNetwork’
  All declared Imports should be used.
File ‘drmdel/libs/drmdel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘readr’ ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rJava’ ‘tools’ ‘xtable’
  All declared Imports should be used.
File ‘dse/libs/dse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.4Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   6.6Mb
File ‘dualtrees/libs/dualtrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘digest’ ‘dplyr’
  All declared Imports should be used.
installed size is 38.9Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs  32.6Mb
Namespaces in Imports field not imported from:
  ‘maptools’ ‘tools’
  All declared Imports should be used.
File ‘dynpred/libs/dynpred.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.5Mb
Namespace in Imports field not imported from: ‘desc’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘FNN’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs       12.5Mb
    shiny_app   1.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   3.7Mb
File ‘EasyABC/libs/EasyABC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’ ‘scales’ ‘xtable’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘base64enc’ ‘knitr’ ‘markdown’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespace in Imports field not imported from: ‘RSQLite’
  All declared Imports should be used.
File ‘ebdbNet/libs/ebdbNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘methods’ ‘mgcv’ ‘rappdirs’ ‘rgdal’ ‘scales’ ‘tools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
File ‘ecolMod/libs/ecolMod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘tnet’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dae’ ‘dplyr’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: replacing previous import ‘sf::st_make_valid’ by ‘lwgeom::st_make_valid’ when loading ‘edbuildmapr’
See ‘/data/gannet/ripley/R/packages/tests-clang/edbuildmapr.Rcheck/00install.out’ for details.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Running ‘test-all.R’ [18s/23s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(eeptools)
  Loading required package: ggplot2
  > 
  > test_check("eeptools")
  ── 1. Failure: moves_calc gets the correct results (@test-calculators.R#210)  ──
  `moves` not equal to `correct_result`.
  Component "sid": Modes: character, numeric
  Component "sid": Attributes: < target is NULL, current is list >
  Component "sid": target is character, current is factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 509 | SKIPPED: 0 | WARNINGS: 29 | FAILED: 1 ]
  1. Failure: moves_calc gets the correct results (@test-calculators.R#210) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
installed size is 113.4Mb
  sub-directories of 1Mb or more:
    libs  112.6Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc       4.4Mb
    extdata   5.1Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘snow’
  All declared Imports should be used.
installed size is 43.3Mb
  sub-directories of 1Mb or more:
    libs  42.3Mb
File ‘eiwild/libs/eiwild.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

> ### Name: sfx_explode
> ### Title: splits line by vertex
> ### Aliases: sfx_explode
> 
> ### ** Examples
> 
> {
+ # Do not run
+ data(emisco)
+ emisco <- emisco[1:100, "V8"]
+ dfco <- sfx_explode(emisco)
+ etm <- to_munich(sdf = dfco)
+ names(etm)
+ class(etm)
+ head(etm$Emissions)
+ head(etm$Street)
+ write.table(x = etm$Emissions, file = paste0(tempfile(), "_Emissions.txt"),
+ row.names = FALSE, sep = " ", quote = FALSE)
+ write.table(x = etm$Street, file = paste0(tempfile(), "_Street.txt"),
+ row.names = FALSE, sep = " ", quote = FALSE)
+ }
Error in to_munich(sdf = dfco) : 
  All emissions must have units. Check ?units::set_units
Execution halted
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘tidyr’
  All declared Imports should be used.
File ‘elec.strat/libs/elec.strat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
File ‘EL/libs/EL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   4.0Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘Rtsne’ ‘uwot’
  All declared Imports should be used.
File ‘EMC/libs/EMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘graphics’ ‘maptools’ ‘rgeos’
  All declared Imports should be used.
File ‘emdist/libs/emdist.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  18.5Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    extdata  10.2Mb
'library' or 'require' calls to packages already attached by Depends:
  ‘clusterSim’ ‘earth’
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘clusterSim’ ‘earth’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.1Mb
File ‘emoa/libs/emoa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.5Mb
Note: found 23639 marked Latin-1 strings
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    lib    4.0Mb
    libs   1.4Mb
File ‘endogMNP/libs/endogMNP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘bitops’ ‘rjson’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SPECIES’ ‘ade4’
  All declared Imports should be used.
File ‘EntropyEstimation/libs/EntropyEstimation.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘DT’ ‘broom’ ‘crosstalk’ ‘dplyr’ ‘ggraph’ ‘igraph’ ‘plotly’
  ‘rmarkdown’ ‘shinythemes’
  All declared Imports should be used.
File ‘enviPick/libs/enviPick.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    doc    3.3Mb
    help   3.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
Namespaces in Imports field not imported from:
  ‘readr’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘colorspace’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘htmlwidgets’
  All declared Imports should be used.
Running ‘testthat.R’ [4s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(epikit)
  > 
  > test_check("epikit")
  ── 1. Failure: case_fatality_rate_df will add a total row to stratified analysis
  `iris_res` not equal to `iris_n`.
  Incompatible type for column `Species`: x character, y factor
  
  ── 2. Failure: case_fatality_rate_df will add a total row to stratified analysis
  `iris_res` not equal to `iris_n`.
  Incompatible type for column `Species`: x character, y factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 107 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: case_fatality_rate_df will add a total row to stratified analysis (@test-proportion.R#152) 
  2. Failure: case_fatality_rate_df will add a total row to stratified analysis and merge CI (@test-proportion.R#173) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘graphics’ ‘knitr’ ‘rmarkdown’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggplot2’ ‘knitr’ ‘pander’
  All declared Imports should be used.
File ‘equivalence/libs/equivalence.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘cubature’ ‘rootSolve’
  All declared Imports should be used.
File ‘erboost/libs/erboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.1Mb
Namespace in Imports field not imported from: ‘signal’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘plyr’ ‘sp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘colorRamps’ ‘colourpicker’ ‘dichromat’ ‘leaflet’
  ‘lwgeom’ ‘raster’ ‘shinycssloaders’ ‘shinydashboard’ ‘shinyjs’ ‘tmap’
  ‘viridis’ ‘zip’
  All declared Imports should be used.
File ‘ESGtoolkit/libs/ESGtoolkit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [6s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(estatapi)
  このサービスは、政府統計総合窓口(e-Stat)のAPI機能を使用していますが、サービスの内容は国によって保証されたものではありません。
  > 
  > test_check("estatapi")
  ── 1. Failure: estat_getStatsData processes the API response as expected  ──────
  estat_getStatsData(...) not identical to readRDS("result_getStatsData.rds").
  Objects equal but not identical
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 22 | SKIPPED: 12 | WARNINGS: 7 | FAILED: 1 ]
  1. Failure: estat_getStatsData processes the API response as expected 
  
  Error: testthat unit tests failed
  Execution halted
File ‘EstHer/libs/EstHer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    libs  25.9Mb
File ‘etasFLP/libs/etasFLP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(etl)
  Loading required package: 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
  
  > 
  > test_check("etl")
  ── 1. Failure: create ETL works (@test-etl.R#114)  ─────────────────────────────
  `create_etl_package\(path, open = FALSE\)` does not match "active project".
  Actual value: "Package: scorecard\\nTitle: What the Package Does \(One Line, Title Case\)\\nVersion: 0\.0\.0\.9000\\nAuthors@R \(parsed\):\\n    \* First Last <first\.last@example\.com> \[aut, cre\] \(YOUR-ORCID-ID\)\\nDescription: What the package does \(one paragraph\)\.\\nLicense: `use_mit_license\(\)`, `use_gpl3_license\(\)` or friends to pick a\\n    license\\nEncoding: UTF-8\\nLazyData: true\\nRoxygen: list\(markdown = TRUE\)\\nRoxygenNote: 7\.0\.0"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 35 | SKIPPED: 2 | WARNINGS: 2 | FAILED: 1 ]
  1. Failure: create ETL works (@test-etl.R#114) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘etm-Ex.R’ failed
The error most likely occurred in:

> ### Name: etm
> ### Title: Computation of the empirical transition matrix
> ### Aliases: etm etm.data.frame
> ### Keywords: survival
> 
> ### ** Examples
> 
> data(sir.cont)
> 
> # Modification for patients entering and leaving a state
> # at the same date
> # Change on ventilation status is considered
> # to happen before end of hospital stay
> sir.cont <- sir.cont[order(sir.cont$id, sir.cont$time), ]
> for (i in 2:nrow(sir.cont)) {
+   if (sir.cont$id[i]==sir.cont$id[i-1]) {
+     if (sir.cont$time[i]==sir.cont$time[i-1]) {
+       sir.cont$time[i-1] <- sir.cont$time[i-1] - 0.5
+     }
+   }
+ }
> 
> ### Computation of the transition probabilities
> # Possible transitions.
> tra <- matrix(ncol=3,nrow=3,FALSE)
> tra[1, 2:3] <- TRUE
> tra[2, c(1, 3)] <- TRUE
> 
> # etm
> tr.prob <- etm(sir.cont, c("0", "1", "2"), tra, "cens", 1)
> 
> tr.prob
Multistate model with 3 transient state(s)
 and 0 absorbing state(s)

Possible transitions:
 from to
    0  1
    0  2
    1  0
    1  2

Estimate of P(1, 183)
  0 1 2
0 0 0 1
1 0 0 1
2 0 0 1

> summary(tr.prob)
Error in object$n.risk[, trs.sep[i, 1]] : subscript out of bounds
Calls: summary -> summary.etm -> ci.transfo -> lapply -> FUN
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘etmCIF_tutorial.Rnw’ using Sweave
Error: processing vignette 'etmCIF_tutorial.Rnw' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘etmCIF_tutorial.Rnw’

SUMMARY: processing the following file failed:
  ‘etmCIF_tutorial.Rnw’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
Running examples in ‘evaluator-Ex.R’ failed
The error most likely occurred in:

> ### Name: exposure_histogram
> ### Title: Display a histogram of losses for a scenario
> ### Aliases: exposure_histogram
> 
> ### ** Examples
> 
> data(mc_simulation_results)
> result <- mc_simulation_results[[1, "results"]]
> exposure_histogram(result)
Error: `data` must be a data frame, or other object coercible by `fortify()`, not a list
Backtrace:
    █
 1. └─evaluator::exposure_histogram(result)
 2.   ├─ggplot2::ggplot(simulation_result, aes(x = .data$ale))
 3.   └─ggplot2:::ggplot.default(simulation_result, aes(x = .data$ale))
 4.     ├─ggplot2::fortify(data, ...)
 5.     └─ggplot2:::fortify.default(data, ...)
Execution halted
Namespaces in Imports field not imported from:
  ‘devtools’ ‘msm’
  All declared Imports should be used.
File ‘evdbayes/libs/evdbayes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Namespaces in Imports field not imported from:
  ‘curl’ ‘openxlsx’ ‘stringr’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
File ‘exactLoglinTest/libs/exactLoglinTest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘clipr’
  All declared Imports should be used.
File ‘exif/libs/exif.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘polynom’
  All declared Imports should be used.
print.cdf : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.cdf: warning in get("x", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.cdf: warning in get("y", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.ogive : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.ogive: warning in get("x", env = environment(x)): partial
  argument match of 'env' to 'envir'
print.ogive: warning in get("y", env = environment(x)): partial
  argument match of 'env' to 'envir'
quantile.expert: warning in formatC(paste(100 * probs, "%", sep = ""),
  format = "fg", wid = 1, digits = dig): partial argument match of
  'wid' to 'width'
MS: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘RColorBrewer’ ‘Rcpp’ ‘e1071’ ‘foreach’ ‘gam’ ‘ggplot2’
  ‘glmnet’ ‘nnet’ ‘polspline’ ‘repmis’ ‘splines’ ‘xgboost’
  All declared Imports should be used.
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  17.5Mb
File ‘extremis/libs/extremis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [31s/41s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fable)
  Loading required package: fabletools
  > 
  > test_check("fable")
  ── 1. Failure: Automatic ETS selection (@test-ets.R#14)  ───────────────────────
  tidy(model(UKLungDeaths[1:24, ], ETS(mdeaths)))$estimate not equal to c(1, 2134).
  names for target but not for current
  
  ── 2. Failure: Manual ETS selection (@test-ets.R#51)  ──────────────────────────
  tidy(refit(fable_fit, USAccDeaths_tbl))$estimate == tidy(fable_fit)$estimate not identical to c(rep(TRUE, 2), rep(FALSE, 12)).
  names for target but not for current
  
  ── 3. Failure: Manual ETS selection (@test-ets.R#62)  ──────────────────────────
  tidy(fable_fit)$estimate[3:14] not identical to c(cmp$level[12], cmp$season[12:2]).
  names for target but not for current
  
  ── 4. Failure: Manual ETS selection (@test-ets.R#87)  ──────────────────────────
  coef$estimate[1:4] not identical to c(0.5, 0.006, 1e-04, 0.975).
  names for target but not for current
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 100 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: Automatic ETS selection (@test-ets.R#14) 
  2. Failure: Manual ETS selection (@test-ets.R#51) 
  3. Failure: Manual ETS selection (@test-ets.R#62) 
  4. Failure: Manual ETS selection (@test-ets.R#87) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘factorcpt/libs/factorcpt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘forcats’ ‘formula.tools’
  All declared Imports should be used.
File ‘factorQR/libs/factorQR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   5.0Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘caTools’ ‘httr’ ‘jsonlite’ ‘rlang’
  All declared Imports should be used.
File ‘falcon/libs/falcon.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   3.5Mb
File ‘fAsianOptions/libs/fAsianOptions.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.4Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Namespace in Imports field not imported from: ‘RobustGaSP’
  All declared Imports should be used.
installed size is 40.4Mb
  sub-directories of 1Mb or more:
    libs  40.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
File ‘FastGP/libs/FastGP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  15.5Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.5Mb
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
File ‘fastmatch/libs/fastmatch.so’:
  Found non-API call to R: ‘match5’
File ‘fastmatch/libs/fastmatch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      7.7Mb
Note: information on .o files is not available
File ‘FastRWeb/libs/null.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Namespace in Imports field not imported from: ‘whisker’
  All declared Imports should be used.
File ‘fBasics/libs/fBasics.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.2Mb
File ‘FBFsearch/libs/FBFsearch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is 47.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  44.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.5Mb
Namespaces in Imports field not imported from:
  ‘usethis’ ‘utils’
  All declared Imports should be used.
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Note: found 3 marked Latin-1 strings
  Note: found 3 marked UTF-8 strings
File ‘FD/libs/FD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘testthat’
  All declared Imports should be used.
File ‘fechner/libs/fechner.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘rvest’ ‘stringi’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘prettycode’
  All declared Imports should be used.
File ‘FFD/libs/FFD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

> ### Name: Extract.ffdf
> ### Title: Reading and writing data.frames (ffdf)
> ### Aliases: Extract.ffdf [.ffdf [<-.ffdf [[.ffdf [[<-.ffdf $.ffdf $<-.ffdf
> ### Keywords: IO data
> 
> ### ** Examples
> 
>    d <- data.frame(a=letters, b=rev(letters), c=1:26)
>    x <- as.ffdf(d)
Error in ff(initdata = initdata, length = length, levels = levels, ordered = ordered,  : 
  vmode 'character' not implemented
Calls: as.ffdf ... do.call -> as.ff -> as.ff.default -> clone.ff -> assign -> ff
Execution halted
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
File ‘fGarch/libs/fGarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
File ‘FIACH/libs/FIACH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘numDeriv’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rappdirs’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘mapproj’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.3Mb
File ‘FisHiCal/libs/FisHiCal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘grid’ ‘png’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
File ‘FitARMA/libs/FitARMA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘XML’ ‘gglasso’ ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   3.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
File ‘flars/libs/flars.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
File ‘flock/libs/flock.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R   6.4Mb
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
File ‘FMStable/libs/FMStable.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
File ‘fOptions/libs/fOptions.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Namespace in Imports field not imported from: ‘decomposedPSF’
  All declared Imports should be used.
File ‘forensim/libs/forensim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rgeos’ ‘viridis’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pkgKitten’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘viridis’
  All declared Imports should be used.
File ‘fpow/libs/fpow.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘fable’ ‘fabletools’ ‘feasts’ ‘ggplot2’ ‘lubridate’ ‘tibble’
  ‘tidyr’ ‘tsibble’ ‘tsibbledata’
  All declared Imports should be used.
File ‘fractional/libs/fractional.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘base’ ‘pbapply’ ‘stringr’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   6.0Mb
Namespaces in Imports field not imported from:
  ‘jsonlite’ ‘rhandsontable’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  ‘shinythemes’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fredr)
  > 
  > test_check("fredr")
  ── 1. Failure: fredr_docs throws errors on invalid endpoints (@test_docs.R#8)  ─
  `fredr_docs(endpoint = "foo")` did not throw an error.
  
  ── 2. Failure: fredr_docs throws errors on invalid endpoints (@test_docs.R#9)  ─
  `fredr_docs(endpoint = "foo", params = TRUE)` did not throw an error.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 65 | SKIPPED: 38 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: fredr_docs throws errors on invalid endpoints (@test_docs.R#8) 
  2. Failure: fredr_docs throws errors on invalid endpoints (@test_docs.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  c_hd_mf.cpp:157:12: warning: explicitly assigning value of variable of type 'Eigen::VectorXd' (aka 'Matrix<double, Dynamic, 1>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/FRegSigCom.Rcheck/00install.out’ for details.
installed size is 68.4Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs  66.6Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   7.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Package suggested but not available for checking: ‘dggrids’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.4Mb
installed size is 61.7Mb
  sub-directories of 1Mb or more:
    libs  61.2Mb
File ‘frontiles/libs/frontiles.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’ ‘neuralnet’ ‘rpart’
  All declared Imports should be used.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
File ‘ftnonpar/libs/ftnonpar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    data  16.2Mb
File ‘fUnitRoots/libs/fUnitRoots.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    libs  32.6Mb
File ‘futureheatwaves/libs/futureheatwaves.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
fuzzyBHexact: warning in round(pvals, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.minus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.plus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(pvals, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(tau, d = 4): partial argument match of
  'd' to 'digits'
probRejTies: no visible binding for global variable ‘nn’
Undefined global functions or variables:
  nn
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    bin  10.0Mb
File ‘gafit/libs/gafit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘maptools’ ‘rgeos’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
File ‘GAMBoost/libs/GAMBoost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘gamlss’
  All declared Imports should be used.
finterp.data.frame: no visible global function definition for
  ‘as.formula’
finterp.data.frame: no visible global function definition for ‘terms’
finterp.data.frame: no visible global function definition for
  ‘model.matrix’
finterp.data.frame: no visible global function definition for
  ‘model.frame’
finterp.default: no visible global function definition for ‘terms’
finterp.default: no visible global function definition for
  ‘model.matrix’
finterp.default: no visible global function definition for
  ‘model.frame’
gamlss.nl: no visible global function definition for ‘nlm’
nl: no visible global function definition for ‘is’
nlgamlss: no visible global function definition for ‘NO’
nlgamlss: no visible global function definition for ‘as.gamlss.family’
nlgamlss: no visible global function definition for ‘nlm’
nlgamlss: no visible global function definition for ‘cov2cor’
summary.nlgamlss: no visible global function definition for ‘coef’
summary.nlgamlss: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  NO as.formula as.gamlss.family coef cov2cor is model.frame
  model.matrix nlm pnorm terms
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "as.formula", "coef", "cov2cor", "model.frame",
             "model.matrix", "nlm", "pnorm", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   4.3Mb
installed size is 116.3Mb
  sub-directories of 1Mb or more:
    libs  115.8Mb
Namespaces in Imports field not imported from:
  ‘methods’ ‘rstantools’
  All declared Imports should be used.
installed size is 82.4Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     79.1Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
File ‘gausscov/libs/gausscov.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  18.7Mb
File ‘gbp/libs/gbp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘gcbd.Rnw’ using Sweave
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
--- failed re-building ‘gcbd.Rnw’

SUMMARY: processing the following file failed:
  ‘gcbd.Rnw’

Error: Vignette re-building failed.
Execution halted
File ‘gconcord/libs/gconcord.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 45.7Mb
  sub-directories of 1Mb or more:
    L8NY18   2.3Mb
    libs    42.1Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
File ‘gdmp/libs/gdmp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
File ‘GEEaSPU/libs/GEEaSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
File ‘gelnet/libs/gelnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘pracma’ ‘rlang’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘NMF’ ‘RColorBrewer’ ‘VennDiagram’ ‘clValid’ ‘data.table’ ‘grid’
  ‘gtools’ ‘pca3d’ ‘rmarkdown’ ‘scales’ ‘shinydashboard’ ‘shinyjs’
  ‘statmod’ ‘stringr’
  All declared Imports should be used.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R  10.2Mb
Namespace in Imports field not imported from: ‘repmis’
  All declared Imports should be used.
File ‘genepi/libs/genepi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  11.8Mb
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
File ‘GenKern/libs/GenKern.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘maptools’ ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘phonTools’ ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   5.2Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   7.2Mb
Namespace in Imports field not imported from: ‘jsonify’
  All declared Imports should be used.
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    data  26.0Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R         9.0Mb
    extdata   1.6Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  13.2Mb
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    data   3.5Mb
Namespaces in Imports field not imported from:
  ‘iterators’ ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘utils’
  All declared Imports should be used.
Running examples in ‘germanpolls-Ex.R’ failed
The error most likely occurred in:

> ### Name: germanpolls
> ### Title: Get data of German polls from wahlrecht.de.
> ### Aliases: germanpolls
> 
> ### ** Examples
> 
> germanpolls(region = "de")
[1] "http://www.wahlrecht.de/umfragen/bundesweite.xml"
 [1] "datum"    "institut" "gebiet"   "cxu"      "spd"      "grn"     
 [7] "fpd"      "lnk"      "afd"      "pir"      "frw"      "son"     
[13] "befragte" "gerundet" "beginn"   "ende"     "methode"  "art_ag"  
[19] "ag_1"     "ag_2"     "status"   "stand"   
Warning: `data_frame()` is deprecated as of tibble 1.1.0.
Please use `tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Error: All columns in a tibble must be vectors.
✖ Column `node` is a `xml_nodeset` object.
Backtrace:
    █
 1. └─germanpolls::germanpolls(region = "de")
 2.   └─germanpolls::get_data_from_xml_de()
 3.     └─tibble::data_frame(row = seq_along(rows), node = rows)
 4.       └─tibble::tibble(!!!quos(...))
 5.         └─tibble:::tibble_quos(xs[!is_null], .rows, .name_repair)
 6.           └─tibble:::check_valid_col(res, col_names[[j]], j)
 7.             └─tibble:::check_valid_cols(set_names(list(x), name))
Execution halted
Namespaces in Imports field not imported from:
  ‘assertthat’ ‘shinydashboard’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘lubridate’ ‘readr’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘bitops’ ‘data.table’ ‘dplyr’ ‘httr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘scales’ ‘stringr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘XML’
  All declared Imports should be used.
File ‘gettz/libs/gettz.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘ggalluvial.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: ggplot2
Quitting from lines 36-46 (ggalluvial.rmd) 
Error: processing vignette 'ggalluvial.rmd' failed with diagnostics:
there is no package called 'plyr'
--- failed re-building ‘ggalluvial.rmd’

--- re-building ‘labels.rmd’ using rmarkdown
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.
Quitting from lines 31-40 (labels.rmd) 
Error: processing vignette 'labels.rmd' failed with diagnostics:
there is no package called 'plyr'
--- failed re-building ‘labels.rmd’

--- re-building ‘order-rectangles.rmd’ using rmarkdown
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.
Quitting from lines 43-46 (order-rectangles.rmd) 
Error: processing vignette 'order-rectangles.rmd' failed with diagnostics:
there is no package called 'plyr'
--- failed re-building ‘order-rectangles.rmd’

SUMMARY: processing the following files failed:
  ‘ggalluvial.rmd’ ‘labels.rmd’ ‘order-rectangles.rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘plotly’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespaces in Imports field not imported from:
  ‘GGEBiplotGUI’ ‘gge’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘grDevices’ ‘scales’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘grid’ ‘rstan’
  All declared Imports should be used.
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  18.7Mb
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘lazyeval’ ‘readr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘gtable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggforce’ ‘webshot’ ‘ztable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘graph’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘sna’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grid’ ‘scales’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘checkmate’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grDevices’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Formula’ ‘GGally’ ‘Hmisc’ ‘colourpicker’ ‘dplyr’ ‘ggpmisc’
  ‘ggpubr’ ‘ggrepel’ ‘ggstance’ ‘grDevices’ ‘grid’ ‘gridExtra’
  ‘lazyeval’ ‘markdown’ ‘plotly’ ‘quantreg’ ‘rlang’ ‘shinyjs’
  ‘survival’ ‘survminer’ ‘table1’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘randomForest’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   3.1Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
Namespaces in Imports field not imported from:
  ‘reshape2’ ‘rosm’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/ggtern.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.8Mb
File ‘GiRaF/libs/GiRaF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘mockery’
  All declared Imports should be used.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
File ‘GLIDE/libs/GLIDE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 49.2Mb
  sub-directories of 1Mb or more:
    libs  48.0Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
File ‘GLMaSPU/libs/GLMaSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
File ‘glmgraph/libs/glmgraph.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 40.9Mb
  sub-directories of 1Mb or more:
    libs  40.2Mb
installed size is 46.6Mb
  sub-directories of 1Mb or more:
    libs  45.7Mb
installed size is 49.2Mb
  sub-directories of 1Mb or more:
    doc         1.2Mb
    libs       45.6Mb
    test_data   1.2Mb
Namespaces in Imports field not imported from:
  ‘AER’ ‘MASS’ ‘Matrix’ ‘censReg’ ‘effects’ ‘foreign’ ‘lme4’ ‘lmtest’
  ‘nnet’ ‘pBrackets’ ‘plm’ ‘pscl’ ‘sandwich’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘cplm’ ‘ggplot2’ ‘rlang’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cplexAPI’
File ‘globalOptTests/libs/globalOptTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Found the following significant warnings:
  Evaluation.cpp:173:9: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/gnmf.Rcheck/00install.out’ for details.
File ‘gnmf/libs/gnmf.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘FactorMatrix.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘FactorMatrix.o’
File ‘gnmf/libs/gnmf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘cluster’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Namespaces in Imports field not imported from:
  ‘rhandsontable’ ‘shiny’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘methods’ ‘stats’
  All declared Imports should be used.
Running examples in ‘gpairs-Ex.R’ failed
The error most likely occurred in:

> ### Name: gpairs
> ### Title: Generalized Pairs Plots
> ### Aliases: gpairs corrgram
> ### Keywords: ts multivariate
> 
> ### ** Examples
> 
> 
> allexamples <- FALSE
> 
> y <- data.frame(A=c(rep("red", 100), rep("blue", 100)),
+                 B=c(rnorm(100),round(rnorm(100,5,1),1)), C=runif(200),
+                 D=c(rep("big", 150), rep("small", 50)),
+                 E=rnorm(200))
> gpairs(y)
Warning in diag.panel(x[, i], names(x)[i], diag.pars, axis.pars, xpos, ypos,  :
  NAs introduced by coercion
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Warning in diag.panel(x[, i], names(x)[i], diag.pars, axis.pars, xpos, ypos,  :
  NAs introduced by coercion
Warning in max(as.numeric(x), na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in diag.panel(x[, i], names(x)[i], diag.pars, axis.pars, xpos, ypos,  :
  NAs introduced by coercion
Warning in min(as.numeric(x), na.rm = TRUE) :
  no non-missing arguments to min; returning Inf
Warning in diag.panel(x[, i], names(x)[i], diag.pars, axis.pars, xpos, ypos,  :
  NAs introduced by coercion
Warning in max(as.numeric(x), na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in diag.panel(x[, i], names(x)[i], diag.pars, axis.pars, xpos, ypos,  :
  NAs introduced by coercion
Warning in min(as.numeric(x), na.rm = TRUE) :
  no non-missing arguments to min; returning Inf
Error in valid.viewport(x, y, width, height, just, gp, clip, xscale, yscale,  : 
  invalid 'xscale' in viewport
Calls: gpairs ... diag.panel -> pushViewport -> viewport -> valid.viewport
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   5.7Mb
File ‘gplm/libs/gplm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    3.5Mb
File ‘GrammR/libs/GrammR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Imap’ ‘Rdpack’ ‘ade4’ ‘doBy’ ‘mclust’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    help   2.4Mb
    libs   3.5Mb
File ‘graphscan/libs/graphscan.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
File ‘groupRemMap/libs/groupRemMap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
File ‘grr/libs/grr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
File ‘gsmoothr/libs/gsmoothr.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   3.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    help   5.1Mb
File ‘GUILDS/libs/GUILDS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Note: possible error in 'lmer(phen1 ~ x.snp + ': unused argument (family = "binomial") 
See ‘/data/gannet/ripley/R/packages/tests-clang/GWAF.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 ‘GWASExactHW/libs/GWASExactHW.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’ ‘spgwr’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.6Mb
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘broom’ ‘dplyr’ ‘ggrepel’ ‘kableExtra’ ‘knitr’ ‘nnet’ ‘plotROC’
  All declared Imports should be used.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
installed size is 134.4Mb
  sub-directories of 1Mb or more:
    R       1.1Mb
    java  132.1Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘gsubfn’ ‘stringr’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
File ‘hapassoc/libs/hapassoc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
File ‘hashFunction/libs/hashFunction.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data  10.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    CWrappers_1.10.2   2.7Mb
    CWrappers_1.10.3   2.6Mb
    CWrappers_1.12.0   3.0Mb
    libs               1.4Mb
File ‘HDGLM/libs/HDGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    libs  37.7Mb
File ‘HDtweedie/libs/HDtweedie.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
Running examples in ‘heemod-Ex.R’ failed
The error most likely occurred in:

> ### Name: define_dsa
> ### Title: Define a Sensitivity Analysis
> ### Aliases: define_dsa define_dsa_
> 
> ### ** Examples
> 
> 
> define_dsa(
+   a, 10, 45,
+   b, .5, 1.5
+ )
Error: All columns in a tibble must be vectors.
✖ Column `dots[i]` is a `lazy_dots` object.
Backtrace:
     █
  1. └─heemod::define_dsa(a, 10, 45, b, 0.5, 1.5)
  2.   └─heemod:::define_dsa_(...)
  3.     ├─base::suppressWarnings(...)
  4.     │ └─base::withCallingHandlers(...)
  5.     ├─dplyr::bind_rows(...)
  6.     │ ├─dplyr:::flatten_bindable(dots_values(...))
  7.     │ └─rlang::dots_values(...)
  8.     ├─stats::setNames(tibble::tibble(dots[i]), names(dots)[i])
  9.     └─tibble::tibble(dots[i])
 10.       └─tibble:::tibble_quos(xs[!is_null], .rows, .name_repair)
 11.         └─tibble:::check_valid_col(res, col_names[[j]], j)
 12.           └─tibble:::check_valid_cols(set_names(list(x), name))
Execution halted
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs  24.1Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘purrr’ ‘tidyverse’
  All declared Imports should be used.
File ‘HiCseg/libs/HiCseg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘MCMCpack’
  All declared Imports should be used.
File ‘hierarchicalSets/libs/hierarchicalSets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc           3.7Mb
    htmlwidgets   4.0Mb
File ‘highD2pop/libs/highD2pop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
    libs   1.2Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    highlight   1.1Mb
    libs        8.7Mb
File ‘hillmakeR/libs/hillmakeR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   5.8Mb
File ‘hit/libs/hit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   4.8Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘methods’ ‘rgl’
  All declared Imports should be used.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’
  All declared Imports should be used.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
File ‘hpa/libs/hpa.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
    Objects: ‘hpaBinary.o’, ‘hpaML.o’, ‘hpaSelection.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  9.3Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   2.5Mb
File ‘hsmm/libs/hsmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 67.9Mb
  sub-directories of 1Mb or more:
    libs  67.4Mb
File ‘htdp/libs/htdp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    htmlwidgets   1.9Mb
    libs          2.9Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data   8.3Mb
    doc    2.1Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
File ‘humaniformat/libs/humaniformat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
File ‘HUM/libs/HUM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   6.1Mb
Namespaces in Imports field not imported from:
  ‘rvest’ ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shiny’ ‘wordcloud2’
  All declared Imports should be used.
File ‘HybridMC/libs/HybridMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘ggplot2’ ‘pander’
  All declared Imports should be used.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   6.0Mb
File ‘iBATCGH/libs/iBATCGH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Registration problems:
  symbol ‘nom1’ in the local frame:
   .C(nom1, as.double(xord), as.integer(length(xord)), as.double(yord), 
       as.double(gridbw), as.integer(length(gridbw)), as.integer(effold), 
       as.integer(neffold), double(length(gridbw)), double(length(gridbw)))
  symbol ‘nom2’ in the local frame:
   .C(nom2, as.double(x), as.integer(n), as.double(y), as.double(bandwidth), 
       as.double(x), as.integer(n), double(n), double(1))
  symbol ‘nom2’ in the local frame:
   .C(nom2, as.double(x), as.integer(n), as.double(y), as.double(bandwidth), 
       as.double(x), as.integer(n), double(n), double(1), double(n))
  symbol ‘nom’ in the local frame:
   .C(nom, as.double(x), as.integer(length(x)), as.double(y), as.double(object$bandwidth), 
       as.double(newdata), as.integer(length(newdata)), double(length(newdata)), 
       double(1))
  symbol ‘nom’ in the local frame:
   .C(nom, as.double(x), as.integer(length(x)), as.double(y), as.double(object$bandwidth), 
       as.double(newdata), as.integer(length(newdata)), double(length(newdata)), 
       double(1), double(length(newdata)))
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
File ‘iBST/libs/iBST.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Mmusculus.UCSC.mm10'
Packages unavailable to check Rd xrefs: ‘BSgenome.Hsapiens.1000genomes.hs37d5’, ‘BSgenome.Mmusculus.UCSC.mm10’
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
File ‘icapca/libs/icapca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
Namespace in Imports field not imported from: ‘coda’
  All declared Imports should be used.
File ‘icemelt/libs/icemelt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
File ‘icensmis/libs/icensmis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  25.2Mb
File ‘identity/libs/identity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
File ‘ieeeround/libs/ieeeround.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘testit’
  All declared Imports should be used.
File ‘ifa/libs/ifa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘xtable’
  All declared Imports should be used.
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  14.4Mb
File ‘IHSEP/libs/IHSEP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 51.2Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    extdata   1.1Mb
    include   3.0Mb
    libs     44.0Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Found the following significant warnings:
  IM4ECpp.cpp:24:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:24:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:22:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:32:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:78: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:78: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/Immigrate.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘haven’
  All declared Imports should be used.
File ‘imputeMDR/libs/imputeMDR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘count_compare’
File ‘imputeMulti/libs/imputeMulti.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lme4’ ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘V8’ ‘assertive’ ‘shinydashboard’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rgeos’
  All declared Imports should be used.
File ‘IndependenceTests/libs/IndependenceTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    help   1.6Mb
Running examples in ‘INDperform-Ex.R’ failed
The error most likely occurred in:

> ### Name: merge_models
> ### Title: Merging two model output tibbles.
> ### Aliases: merge_models
> 
> ### ** Examples
> 
> # Using some models of the Baltic Sea demo data:
> # Merging GAM and GAMM tibbles
> test_ids <- 47:50 # choose subset
> gam_tbl <- model_gam_ex[test_ids,]
> gamm_tbl <- model_gamm(ind_init_ex[test_ids,], filter= gam_tbl$tac)
Error in model_gamm(ind_init_ex[test_ids, ], filter = gam_tbl$tac) : 
  No IND~pressure GAMM could be fitted! Check if you chose the correct error distribution (default is gaussian()).
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
File ‘influenceR/libs/influenceR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ca’
  All declared Imports should be used.
File ‘INSPIRE/libs/INSPIRE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘flextable’ ‘officer’
  All declared Imports should be used.
File ‘Interact/libs/Interact.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
Namespaces in Imports field not imported from:
  ‘EValue’ ‘tidyverse’
  All declared Imports should be used.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
Namespaces in Imports field not imported from:
  ‘chron’ ‘zoo’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘bsplus’ ‘colourpicker’ ‘kableExtra’ ‘markdown’ ‘reshape2’
  ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’
File ‘iotools/libs/iotools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘GlobalOptions’ ‘dplyr’ ‘testthat’
  All declared Imports should be used.
File ‘ipfp/libs/ipfp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Namespace in Imports field not imported from: ‘seqinr’
  All declared Imports should be used.
File ‘iRafNet/libs/iRafNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  rf.c:492:17: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/iRF.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘irr’
  All declared Imports should be used.
File ‘ISBF/libs/ISBF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘colorRamps’ ‘virtualspecies’
  All declared Imports should be used.
File ‘isingLenzMC/libs/isingLenzMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.2Mb
File ‘isocir/libs/isocir.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
File ‘ISR3/libs/ISR3.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘pangaear’ ‘rcrossref’ ‘rgdal’ ‘stringr’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘acf.Rmd’ using rmarkdown
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.
--- finished re-building ‘acf.Rmd’

--- re-building ‘inspect.Rmd’ using rmarkdown
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.
Quitting from lines 101-106 (inspect.Rmd) 
Error: processing vignette 'inspect.Rmd' failed with diagnostics:
non-conformable arrays
--- failed re-building ‘inspect.Rmd’

--- re-building ‘test.Rmd’ using rmarkdown
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.
Quitting from lines 187-200 (test.Rmd) 
Error: processing vignette 'test.Rmd' failed with diagnostics:
non-conformable arrays
--- failed re-building ‘test.Rmd’

SUMMARY: processing the following files failed:
  ‘inspect.Rmd’ ‘test.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          21.0Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘ggExtra’ ‘ggplot2’ ‘grid’ ‘gridExtra’ ‘mcmcplots’
  All declared Imports should be used.
File ‘JASPAR/libs/JASPAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/JavaGD.Rcheck/00install.out’ for details.
File ‘JavaGD/libs/JavaGD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘GA’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘png’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘BurStFin’ ‘MASS’ ‘fAssets’ ‘timeDate’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   7.6Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘MASS’ ‘PMCMR’ ‘R6’ ‘ROCR’
  ‘afex’ ‘car’ ‘emmeans’ ‘ggridges’ ‘lavaan’ ‘multcomp’ ‘mvnormtest’
  ‘nnet’ ‘psych’ ‘vcd’ ‘vcdExtra’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   5.0Mb
Found the following significant warnings:
  jomo1clmmC.c:105:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo1clmmhrC.c:107:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmC.c:128:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmhrC.c:132:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomooprobitC.c:84:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/jomo.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
File ‘jpeg/libs/jpeg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘survC1’
  All declared Imports should be used.
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   6.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
File ‘kappalab/libs/kappalab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stinepack’
  All declared Imports should be used.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  16.6Mb
File ‘Kendall/libs/Kendall.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lme4’ ‘metafor’ ‘nlme’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
File ‘KERE/libs/KERE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
File ‘KernSmoothIRT/libs/KernSmoothIRT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘gplots’ ‘wesanderson’
  All declared Imports should be used.
File ‘kml/libs/kml.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Package in Depends field not imported from: ‘cluster’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespaces in Imports field not imported from:
  ‘FNN’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘psycho’ ‘rhandsontable’
  ‘shiny’
  All declared Imports should be used.
File ‘kolmim/libs/kolmim.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘mice’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tibble’
  All declared Imports should be used.
File ‘kriging/libs/kriging.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  17.7Mb
File ‘labdsv/libs/labdsv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.3Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   8.4Mb
File ‘LakeMetabolizer/libs/LakeMetabolizer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  W_gamma_Cpp.cpp:14:39: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/LambertW.Rcheck/00install.out’ for details.
File ‘LambertW/libs/LambertW.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Namespaces in Imports field not imported from:
  ‘callr’ ‘collections’ ‘repr’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    2.0Mb
    help   1.1Mb
File ‘lars/libs/lars.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Namespaces in Imports field not imported from:
  ‘ReinforcementLearning’ ‘ggplot2’ ‘grDevices’ ‘h2o’ ‘lubridate’
  ‘magrittr’ ‘openssl’ ‘readr’ ‘stringr’
  All declared Imports should be used.
File ‘lbfgsb3/libs/lbfgsb3.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  ./lda_svi.h:1:9: warning: '_lda_svi_guard' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
See ‘/data/gannet/ripley/R/packages/tests-clang/lda.svi.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘tm’
  All declared Imports should be used.
File ‘leaderCluster/libs/leaderCluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘htmlwidgets’ ‘jsonlite’ ‘sf’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘leaflet’
  All declared Imports should be used.
File ‘leaps/libs/leaps.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Error(s) in re-building vignettes:
--- re-building ‘liayson.Rnw’ using Sweave

Error: processing vignette 'liayson.Rnw' failed with diagnostics:
 chunk 1 
Error in bmRequest(request = request, verbose = verbose) : 
  Service Unavailable (HTTP 503).

--- failed re-building ‘liayson.Rnw’

SUMMARY: processing the following file failed:
  ‘liayson.Rnw’

Error: Vignette re-building failed.
Execution halted
File ‘LiblineaR.ACF/libs/LiblineaR.ACF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  clang-10: warning: -lOPF: 'linker' input unused [-Wunused-command-line-argument]
  clang-10: warning: -lm: 'linker' input unused [-Wunused-command-line-argument]
See ‘/data/gannet/ripley/R/packages/tests-clang/LibOPF.Rcheck/00install.out’ for details.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    extdata   1.2Mb
    libs      7.8Mb
Running ‘testthat.R’ [117s/227s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(lidR)
  Loading required package: raster
  Loading required package: sp
  > 
  > options(lidR.progress = FALSE)
  > 
  > test_check("lidR")
  ── 1. Failure: catalog_apply automerge works with in memory POINTS (@test-catalo
  projection(req2) not equal to "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clrk66 +units=m +no_defs".
  1/1 mismatches
  x[1]: "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clr
  x[1]: k66 +units=m +no_defs "
  y[1]: "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clr
  y[1]: k66 +units=m +no_defs"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 971 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: catalog_apply automerge works with in memory POINTS (@test-catalog_apply-automerge.R#171) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
Namespace in Imports field not imported from: ‘ddpcr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘data.table’ ‘e1071’ ‘fastmatch’
  All declared Imports should be used.
File ‘linERR/libs/linERR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  10.4Mb
File ‘listdtr/libs/listdtr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
File ‘ljr/libs/ljr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        2.4Mb
    libs      20.7Mb
    testdata   1.6Mb
lmec: warning in qr.Q(qrZ, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: warning in qr.Q(qra, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: no visible global function definition for ‘lm’
lmec: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘dnorm’
lmec : vtrnorm2: no visible global function definition for ‘runif’
lmec : vtrnorm2: no visible global function definition for ‘qnorm’
lmec : vtrnorm2: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘rnorm’
lmec: no visible global function definition for ‘ar’
Undefined global functions or variables:
  ar dnorm lm pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "ar", "dnorm", "lm", "pnorm", "qnorm", "rnorm",
             "runif")
to your NAMESPACE file.
File ‘lmeNBBayes/libs/lmeNBBayes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘boot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
File ‘lmPerm/libs/lmPerm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
File ‘loe/libs/loe.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘modules’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘distr’
  All declared Imports should be used.
Package in Depends field not imported from: ‘logcondens’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘logisticPCA/libs/logisticPCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 28.1Mb
  sub-directories of 1Mb or more:
    libs  26.4Mb
Namespace in Imports field not imported from: ‘futile.options’
  All declared Imports should be used.
File ‘lorec/libs/lorec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      1.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
File ‘LPStimeSeries/libs/LPStimeSeries.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 143 marked Latin-1 strings
  Note: found 833 marked UTF-8 strings
installed size is 52.0Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  49.4Mb
Namespace in Imports field not imported from: ‘lavaan’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
File ‘ltbayes/libs/ltbayes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   4.0Mb
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘raster’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.1Mb
    libs   2.0Mb
File ‘lxb/libs/lxb.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘utils’
  All declared Imports should be used.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    TS_files     5.9Mb
    base_files   6.3Mb
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.

Requires orphaned package: ‘etm’
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘cmprsk’ ‘colorspace’ ‘etm’ ‘fracdiff’ ‘gtable’ ‘munsell’
  ‘numDeriv’ ‘plyr’ ‘quadprog’ ‘scales’ ‘timeDate’ ‘tseries’ ‘zoo’
  All declared Imports should be used.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs   7.5Mb
File ‘magree/libs/magree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs  19.5Mb
File ‘MAMSE/libs/MAMSE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
installed size is 46.9Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.2Mb
    htmlwidgets   2.0Mb
    libs         42.0Mb
File ‘mapfit/libs/mapfit.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rgdal’ ‘rlang’ ‘testthat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘betareg’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘kableExtra’ ‘knitr’
  All declared Imports should be used.
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs  11.7Mb
File ‘mateable/libs/mateable.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
File ‘MaXact/libs/MaXact.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘effsize’ ‘psych’
  All declared Imports should be used.
File ‘mbrglm/libs/mbrglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  12.8Mb
File ‘mcemGLM/libs/mcemGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
installed size is 52.1Mb
  sub-directories of 1Mb or more:
    libs  51.1Mb
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
Namespaces in Imports field not imported from:
  ‘parallelMap’ ‘reshape2’
  All declared Imports should be used.
File ‘mco/libs/mco.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘bayesplot’ ‘methods’ ‘purrr’
  All declared Imports should be used.
File ‘mcr/libs/mcr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘covr’ ‘curl’ ‘devtools’ ‘gh’ ‘git2r’ ‘httr’ ‘knitr’ ‘openssl’
  ‘pkgbuild’ ‘rlang’ ‘rmarkdown’ ‘roxygen2’ ‘spelling’ ‘testthat’
  ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘datasets’ ‘dplyr’ ‘psych’ ‘shiny’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Namespace in Imports field not imported from: ‘mds’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      1.3Mb
File ‘meboot/libs/meboot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  lightextinction.cpp:74:63: warning: explicitly assigning value of variable of type 'Rcpp::String' to itself [-Wself-assign-overloaded]
  lightextinction.cpp:85:64: warning: explicitly assigning value of variable of type 'Rcpp::String' to itself [-Wself-assign-overloaded]
  transpiration.cpp:18:28: warning: result of '10^3' is 9; did you mean '1e3'? [-Wxor-used-as-pow]
See ‘/data/gannet/ripley/R/packages/tests-clang/medfate.Rcheck/00install.out’ for details.
installed size is 35.2Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs  31.0Mb
Error(s) in re-building vignettes:
--- re-building ‘medflex.Rnw’ using Sweave
Loading required package: multcomp
Loading required package: mvtnorm
Loading required package: survival
Loading required package: TH.data
Loading required package: MASS

Attaching package: 'TH.data'

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

    geyser

medflex 0.6-6: Flexible Mediation Analysis Using Natural Effect Models
Please report bugs here: github.com/jmpsteen/medflex/issues
attbin01 
  0.3959 
attbin11 
   0.352 
Loading required package: carData
att0 
1.34 
att0 + att0:att1 
            1.44 
att1 
1.20 
att1 + att0:att1 
            1.29 
att0 + att1 + att0:att1 
                   1.73 
Effect decomposition on the scale of the linear predictor
conditional on: gender, educ, age 
with x* = 0, x = 1

Effect decomposition on exp(scale of the linear predictor)
conditional on: gender, educ, age 
with x* = 0, x = 1

Effect decomposition on the scale of the linear predictor
conditional on: gender, educ, age 
with x* = 0, x = 1

Effect decomposition on exp(scale of the linear predictor)
conditional on: gender, educ, age 
with x* = 0, x = 1

Error: processing vignette 'medflex.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'medflex.tex' failed.
LaTeX errors:
! LaTeX Error: File `tkz-berge.sty' not found.

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

! Emergency stop.
<read *> 
         
l.12 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'medflex.Rnw'

--- re-building ‘sandwich.Rnw’ using Sweave
--- finished re-building ‘sandwich.Rnw’

SUMMARY: processing the following file failed:
  ‘medflex.Rnw’

Error: Vignette re-building failed.
Execution halted
File ‘MediaK/libs/MediaK.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘ggplot2’ ‘lavaan’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘RGtk2’ ‘RNifti’ ‘cairoDevice’ ‘gtools’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘RODBC’ ‘dplyr’ ‘foreign’ ‘formattable’ ‘ggplot2’
  ‘haven’ ‘mem’ ‘openxlsx’ ‘plotly’ ‘readxl’ ‘shinyBS’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringi’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shinyBS’ ‘shinycssloaders’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   2.9Mb
Namespace in Imports field not imported from: ‘urca’
  All declared Imports should be used.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   6.6Mb
installed size is 123.4Mb
  sub-directories of 1Mb or more:
    libs  122.8Mb
Namespaces in Imports field not imported from:
  ‘ggrepel’ ‘reshape’ ‘svglite’
  All declared Imports should be used.
Running ‘testthat.R’ [188s/466s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > suppressPackageStartupMessages(library(metacoder))
  > 
  > test_check("metacoder")
  ── 1. Failure: Summing counts per taxon (@test--calculations.R#103)  ───────────
  sum(x$data$tax_data$`700035949`) not equal to result$`700035949`[1].
  names for current but not for target
  
  ── 2. Failure: Summing counts per taxon (@test--calculations.R#126)  ───────────
  `total_counts` not equal to result$total[1].
  names for current but not for target
  
  ── 3. Failure: Parsing the UNITE general release fasta (@test--parsers_and_write
  result$data$tax_data$unite_seq[5] not equal to "CCAAATCATGTCTCCCGGCCGCAAGGCAGGTGCAGGCGTTTAACCCTTTGTGAACCAAAAAACCTTTCGCTTCGGCAGCAGCTCGGTTGGAGACAGCCTCTGTGTCAGCCTGCCGCTAGCACCAATTATCAAAACTTGCGGTTAGCAACATTGTCTGATTACCAAATTTTCGAATGAAAATCAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAACGCGATAGTTAATGTGAATTGCAGAATTCAGTGAATCATCGAGTCTTTGAACGCACATTGCGCCCATTGGTATTCCATTGGGCATGTCTGTTTGAGCGTCATTACAACCCTCGGTCACCACCGGTTTTGAGCGAGCAGGGTCTTCGGATCCAGCTGGCTTTAAAGTTGTAAGCTCTGCTGGCTGCTCGGCCCAACCAGAACATAGTAAAATCATGCTTGTTCAAGGTTCGCGGTCGAAGCGGTACGGCCTGAACAATACCTACCACCTCTTAGG".
  names for target but not for current
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 93 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Summing counts per taxon (@test--calculations.R#103) 
  2. Failure: Summing counts per taxon (@test--calculations.R#126) 
  3. Failure: Parsing the UNITE general release fasta (@test--parsers_and_writers.R#119) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘metafolio/libs/metafolio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘DT’ ‘GEOmetadb’ ‘RMySQL’ ‘RSQLite’ ‘gplots’ ‘pheatmap’
  ‘readr’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘foreign’ ‘gplots’ ‘httr’ ‘jsonlite’ ‘knitr’ ‘lmerTest’
  ‘magrittr’ ‘mgcv’ ‘repmis’ ‘reshape2’ ‘rmarkdown’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘metan_start.Rmd’ using rmarkdown
[]=====================================================[]
[] Multi-Environment Trial Analysis (metan) v1.4.0     []
[] Author: Tiago Olivoto                               []
[] Type citation('metan') to know how to cite metan    []
[] Type vignette('metan_start') for a short tutorial   []
[] Visit http://bit.ly/2TIq6JE for a complete tutorial []
[]=====================================================[]
No issues detected while inspecting data.
Quitting from lines 133-134 (metan_start.Rmd) 
Error: processing vignette 'metan_start.Rmd' failed with diagnostics:
No common type for `..1$Y` <character> and `..2$Y` <integer>.
--- failed re-building ‘metan_start.Rmd’

SUMMARY: processing the following file failed:
  ‘metan_start.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rlang’ ‘rmarkdown’ ‘testthat’
  All declared Imports should be used.
installed size is 124.0Mb
  sub-directories of 1Mb or more:
    libs  123.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   4.2Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   2.5Mb
File ‘MEtest/libs/MEtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 30.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.1Mb
    libs  25.6Mb
    misc   1.1Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
File ‘mewAvg/libs/mewAvg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    libs  27.8Mb
File ‘mgarchBEKK/libs/mgarchBEKK.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  19.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
File ‘mhsmm/libs/mhsmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘copula’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggiraph’ ‘ggplot2’ ‘grid’ ‘gtools’ ‘scales’ ‘shinyBS’
  ‘shinyWidgets’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mipfp’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘softImpute’
  All declared Imports should be used.
Running examples in ‘MIMSunit-Ex.R’ failed
The error most likely occurred in:

> ### Name: import_mhealth_csv
> ### Title: Import raw multi-channel accelerometer data stored in mHealth
> ###   Specification
> ### Aliases: import_mhealth_csv
> 
> ### ** Examples
> 
>   default_ops = options()
>   options(digits.secs=3)
>   # Use the sample mhealth csv file provided by the package
>   filepath = system.file('extdata', 'mhealth.csv', package='MIMSunit')
>   filepath
[1] "/data/gannet/ripley/R/packages/tests-clang/MIMSunit.Rcheck/MIMSunit/extdata/mhealth.csv"
> 
>   # Load the file
>   df = import_mhealth_csv(filepath)
Error: Assigned data `as.character(df[, factor_cols])` must be compatible with existing data.
✖ Existing data has 5000 rows.
✖ Assigned data has 0 rows.
ℹ Only vectors of size 1 are recycled.
Backtrace:
    █
 1. └─MIMSunit::import_mhealth_csv(filepath)
 2.   ├─base::`[<-`(`*tmp*`, , factor_cols, value = character(0))
 3.   └─tibble:::`[<-.tbl_df`(`*tmp*`, , factor_cols, value = character(0))
 4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 5.       └─tibble:::vectbl_recycle_rhs(...)
 6.         └─base::tryCatch(...)
 7.           └─base:::tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)
Execution halted
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
Namespaces in Imports field not imported from:
  ‘DiceDesign’ ‘MaxPro’ ‘doSNOW’ ‘gmp’ ‘jpeg’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘markdown’ ‘metafor’
  All declared Imports should be used.
File ‘minpack.lm/libs/minpack.lm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cdf.pval: no visible global function definition for ‘median’
cdf.pval: no visible binding for global variable ‘ecdf’
find_hits: no visible global function definition for ‘na.omit’
mad.scores: no visible global function definition for ‘as.formula’
mad.scores: no visible binding for global variable ‘median’
mad.scores: no visible binding for global variable ‘mad’
rm.outliers: no visible global function definition for ‘as.formula’
rm.outliers: no visible binding for global variable ‘median’
rm.outliers: no visible binding for global variable ‘mad’
Undefined global functions or variables:
  as.formula ecdf mad median na.omit
Consider adding
  importFrom("stats", "as.formula", "ecdf", "mad", "median", "na.omit")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘dendextend’ ‘npmv’ ‘utils’
  All declared Imports should be used.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   8.1Mb
File ‘MiSPU/libs/MiSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  simcensor.cpp:91:16: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:91:41: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:95:17: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/missDeaths.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘mcmcr’
  All declared Imports should be used.
installed size is 44.8Mb
  sub-directories of 1Mb or more:
    libs  42.5Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
File ‘mixedMem/libs/mixedMem.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rjags’
  All declared Imports should be used.
File ‘mkde/libs/mkde.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
File ‘mlbench/libs/mlbench.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘iterators’ ‘parallel’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DiscriMiner’ ‘MASS’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘klaR’
  ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
File ‘MLEcens/libs/MLEcens.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
File ‘mlmc/libs/mlmc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘DT’ ‘data.table’ ‘e1071’ ‘mlr3’ ‘mlr3learners’ ‘mlr3measures’ ‘plyr’
  ‘purrr’ ‘ranger’ ‘readxl’ ‘shinyWidgets’ ‘shinyalert’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stats’ ‘stringr’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
Namespaces in Imports field not imported from:
  ‘QuantPsyc’ ‘corrgram’ ‘dplyr’ ‘forecast’ ‘psych’ ‘shinyAce’
  All declared Imports should be used.
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
Namespace in Imports field not imported from: ‘plotrix’
  All declared Imports should be used.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘e1071’ ‘nnet’ ‘shiny’ ‘stats’
  All declared Imports should be used.
File ‘mnormpow/libs/mnormpow.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘sads’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rmisc’ ‘amap’ ‘fields’ ‘matrixStats’ ‘mco’ ‘miscTools’ ‘plyr’
  ‘reshape2’
  All declared Imports should be used.
File ‘ModelGood/libs/ModelGood.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘lattice’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘BioStatR’ ‘ggplot2’
  All declared Imports should be used.
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    doc  23.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    libs   4.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/MomTrunc.Rcheck/00install.out’ for details.
File ‘MonetDB.R/libs/MonetDB.R.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ratelimitr’
  All declared Imports should be used.
File ‘monreg/libs/monreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   9.9Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   9.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.8Mb
File ‘mpbart/libs/mpbart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 82.6Mb
  sub-directories of 1Mb or more:
    R             1.1Mb
    libs         78.8Mb
    mathematica   1.5Mb
File ‘mpmi/libs/mpmi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
export.summary.mpm: warning in complex(real = x$Rows[, FdimsR[1]], imag
  = x$Rows[, FdimsR[2]]): partial argument match of 'imag' to
  'imaginary'
export.summary.mpm: warning in complex(real = x$Columns[, FdimsC[1]],
  imag = x$Columns[, FdimsC[2]]): partial argument match of 'imag' to
  'imaginary'
.onAttach: no visible global function definition for
  ‘packageDescription’
export.summary.mpm: no visible global function definition for
  ‘write.table’
mpm: no visible binding for global variable ‘median’
plot.mpm: no visible global function definition for ‘rainbow’
plot.mpm: no visible global function definition for ‘quantile’
plot.mpm: no visible global function definition for ‘par’
plot.mpm: no visible global function definition for ‘points’
plot.mpm: no visible global function definition for ‘smoothScatter’
plot.mpm: no visible global function definition for ‘colorRampPalette’
plot.mpm: no visible global function definition for ‘symbols’
plot.mpm: no visible global function definition for ‘text’
plot.mpm: no visible global function definition for ‘lines’
plot.mpm: no visible global function definition for ‘box’
Undefined global functions or variables:
  box colorRampPalette lines median packageDescription par points
  quantile rainbow smoothScatter symbols text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("graphics", "box", "lines", "par", "points",
             "smoothScatter", "symbols", "text")
  importFrom("stats", "median", "quantile")
  importFrom("utils", "packageDescription", "write.table")
to your NAMESPACE file.
File ‘mp/libs/mp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
File ‘MRCE/libs/MRCE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  15.2Mb
File ‘mrfse/libs/mrfse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
File ‘MRH/libs/MRH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘moments’ ‘mvtnorm’
  All declared Imports should be used.
installed size is 31.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.1Mb
    libs  28.4Mb
installed size is 51.6Mb
  sub-directories of 1Mb or more:
    libs  51.2Mb
File ‘MSGLasso/libs/MSGLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs  18.6Mb
Namespace in Imports field not imported from: ‘amap’
  All declared Imports should be used.
File ‘MTS/libs/MTS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘capushe’ ‘shiny’
  All declared Imports should be used.
File ‘muhaz/libs/muhaz.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
File ‘MultiBD/libs/MultiBD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘cowsay’
  All declared Imports should be used.
installed size is 83.5Mb
  sub-directories of 1Mb or more:
    libs  83.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
File ‘multinomRob/libs/multinomRob.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    libs  28.9Mb
File ‘MVB/libs/MVB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘utils’
  All declared Imports should be used.
File ‘mvrtn/libs/mvrtn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    java  13.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.5Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
File ‘namespace/libs/namespace.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Error(s) in re-building vignettes:
--- re-building ‘exploring-imputed-values.Rmd’ using rmarkdown
Quitting from lines 78-87 (exploring-imputed-values.Rmd) 
Error: processing vignette 'exploring-imputed-values.Rmd' failed with diagnostics:
`i` must have one dimension, not 2.
--- failed re-building ‘exploring-imputed-values.Rmd’

--- re-building ‘getting-started-w-naniar.Rmd’ using rmarkdown
Quitting from lines 284-292 (getting-started-w-naniar.Rmd) 
Error: processing vignette 'getting-started-w-naniar.Rmd' failed with diagnostics:
`i` must have one dimension, not 2.
--- failed re-building ‘getting-started-w-naniar.Rmd’

--- re-building ‘naniar-visualisation.Rmd’ using rmarkdown
--- finished re-building ‘naniar-visualisation.Rmd’

--- re-building ‘replace-with-na.Rmd’ using rmarkdown
Quitting from lines 43-52 (replace-with-na.Rmd) 
Error: processing vignette 'replace-with-na.Rmd' failed with diagnostics:
No common type for `y` <character> and `y` <double>.
--- failed re-building ‘replace-with-na.Rmd’

--- re-building ‘special-missing-values.Rmd’ using rmarkdown
--- finished re-building ‘special-missing-values.Rmd’

SUMMARY: processing the following files failed:
  ‘exploring-imputed-values.Rmd’ ‘getting-started-w-naniar.Rmd’
  ‘replace-with-na.Rmd’

Error: Vignette re-building failed.
Execution halted
File ‘nanop/libs/nanop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.9Mb
Namespace in Imports field not imported from: ‘tuneR’
  All declared Imports should be used.
File ‘nbpMatching/libs/nbpMatching.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘bookdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Deriv’ ‘compiler’ ‘stringi’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.0Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.
File ‘NeatMap/libs/NeatMap.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘nMDS_R.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘nMDS_R.o’
File ‘NeatMap/libs/NeatMap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ez’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘igraph’
  All declared Imports should be used.
File ‘NetComp/libs/NetComp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘mvrtn’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Namespace in Imports field not imported from: ‘clue’
  All declared Imports should be used.
File ‘NetPreProc/libs/NetPreProc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   7.0Mb
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
File ‘networksis/libs/networksis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
File ‘neuroim/libs/neuroim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘htmlTable’ ‘lme4’ ‘stringi’
  All declared Imports should be used.
File ‘neuRosim/libs/neuRosim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘xml2’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
File ‘nice/libs/nice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    CppCode        1.1Mb
    R              6.1Mb
    classic-bugs   1.6Mb
    include        5.7Mb
    libs          17.2Mb
    tests          1.6Mb
Namespace in Imports field not imported from: ‘rjson’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.3Mb
Namespace in Imports field not imported from: ‘deSolve’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘jsonlite’
  All declared Imports should be used.
File ‘nmfgpu4R/libs/nmfgpu4R.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘BiocManager’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘KernelKnn’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘uroot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘multicool’
  All declared Imports should be used.
File ‘nnls/libs/nnls.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘XML’ ‘choroplethr’ ‘choroplethrMaps’ ‘data.table’
  ‘forcats’ ‘hurricaneexposure’ ‘plyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘arrow’
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
File ‘noncompliance/libs/noncompliance.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘e1071’ ‘pROC’ ‘purrr’ ‘randomForest’ ‘rlang’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
File ‘nontarget/libs/nontarget.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
File ‘norm/libs/norm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Namespace in Imports field not imported from: ‘rts’
  All declared Imports should be used.
File ‘NPsimex/libs/NPsimex.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘xgboost’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’ ‘base’ ‘graphics’ ‘parallel’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forecast’ ‘rlang’ ‘tsibble’ ‘viridis’
  All declared Imports should be used.
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    doc    7.4Mb
    libs  20.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.4Mb
File ‘nws/R/zzz.R’:
  .onLoad calls:
    require(methods)

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

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

Found the following assignments to the global environment:
File ‘nws/R/workerLoop.R’:
  assign("SleighName", displayName, globalenv())
  assign("SleighNws", nws, globalenv())
  assign("SleighUserNws", userNws, globalenv())
  assign("SleighRank", rank, globalenv())
  assign("SleighWorkerCount", workerCount, globalenv())
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘obliclus/libs/obliclus.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘random_cluster_C.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘random_cluster_C.o’
File ‘obliclus/libs/obliclus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘units’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.5Mb
    test_files   4.2Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    doc    2.3Mb
    help   2.7Mb
    libs   4.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘graphics’
  All declared Imports should be used.
File ‘olctools/libs/olctools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 35.7Mb
  sub-directories of 1Mb or more:
    libs  34.0Mb
Namespaces in Imports field not imported from:
  ‘e1071’ ‘fs’ ‘pdp’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘safer’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.4Mb
File ‘onemap/libs/onemap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘digest’ ‘dplyr’ ‘miniUI’ ‘text2vec’
  All declared Imports should be used.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   6.3Mb
Running ‘testthat.R’ [35s/115s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(OpenLand)
  > 
  > test_check("OpenLand")
  ── 1. Error: (unknown) (@test_generalfunctions.R#29)  ──────────────────────────
  package 'rgdal' is not available
  Backtrace:
    1. base::lapply(...)
    2. OpenLand:::FUN(X[[i]], ...)
    4. raster::writeRaster(...)
    5. raster:::.local(x, filename, ...)
    6. raster:::.writeGDALall(...)
    7. raster:::.startGDALwriting(...)
    8. raster:::.getGDALtransient(...)
    9. raster:::.isSupportedFormat(gdalfiletype)
   10. raster:::.isSupportedGDALFormat(dname)
   11. raster:::.requireRgdal()
  
  ── 2. Error: (unknown) (@test_inputrasters.R#5)  ───────────────────────────────
  package 'rgdal' is not available
  Backtrace:
    1. base::lapply(...)
    2. OpenLand:::FUN(X[[i]], ...)
    4. raster::writeRaster(...)
    5. raster:::.local(x, filename, ...)
    6. raster:::.writeGDALall(...)
    7. raster:::.startGDALwriting(...)
    8. raster:::.getGDALtransient(...)
    9. raster:::.isSupportedFormat(gdalfiletype)
   10. raster:::.isSupportedGDALFormat(dname)
   11. raster:::.requireRgdal()
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 96 | SKIPPED: 0 | WARNINGS: 24 | FAILED: 2 ]
  1. Error: (unknown) (@test_generalfunctions.R#29) 
  2. Error: (unknown) (@test_inputrasters.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 212.7Mb
  sub-directories of 1Mb or more:
    R         2.5Mb
    libs    202.6Mb
    models    4.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
possible bashism in configure line 52 (test -a/-o):
  if test ${java_version_maj} -ge 5 || \
      test ${java_version_maj} -eq 1 -a ${java_version_min} -ge 5;
possible bashism in configure line 34 ($(OS|MACH)TYPE):
    case "$OSTYPE" in "darwin"*)
  possible bashism in configure line 40 (should be '.', not 'source'):
      source autobrew
  possible bashism in configure line 79 ($(OS|MACH)TYPE):
  case "$OSTYPE" in
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      6.3Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
File ‘OptGS/libs/OptGS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘geometry’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.9Mb
Namespaces in Imports field not imported from:
  ‘boot’ ‘splines’
  All declared Imports should be used.
File ‘optpart/libs/optpart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nr' to 'nrow'
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nc' to 'ncol'
bgmm: no visible global function definition for ‘ecdf’
bgmm : SplineGMM: no visible global function definition for
  ‘constrOptim’
blr: no visible global function definition for ‘ecdf’
blr: no visible global function definition for ‘constrOptim’
blr: no visible global function definition for ‘lm’
parentcdf : combinations: no visible global function definition for
  ‘combn’
parentcdf : solver: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  combn constrOptim ecdf lm uniroot
Consider adding
  importFrom("stats", "constrOptim", "ecdf", "lm", "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
File ‘ordinalpattern/libs/ordinalpattern.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘OriGen/libs/OriGen.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_rewind’, possibly from ‘rewind’ (Fortran)
    Object: ‘OriGen.o’
File ‘OriGen/libs/OriGen.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    nifti   3.8Mb
est.lme : <anonymous>: warning in rank(iru, ties = "min"): partial
  argument match of 'ties' to 'ties.method'
est.lme : <anonymous>: no visible global function definition for ‘lme’
est.lme : <anonymous>: no visible global function definition for
  ‘VarCorr’
guo: no visible global function definition for ‘p.adjust’
guo: no visible global function definition for ‘na.omit’
pttest : ptest: no visible global function definition for ‘na.omit’
srt : <anonymous>: no visible global function definition for
  ‘rowttests’
Undefined global functions or variables:
  VarCorr lme na.omit p.adjust rowttests
Consider adding
  importFrom("stats", "na.omit", "p.adjust")
to your NAMESPACE file.
File ‘orQA/libs/orQA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  19.3Mb
File ‘osDesign/libs/osDesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   7.9Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
Package suggested but not available for checking: ‘Rcplex’
Namespace in Imports field not imported from: ‘quantreg’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   2.9Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Namespace in Imports field not imported from: ‘ape’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Namespace in Imports field not imported from: ‘GenomicAlignments’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘network’ ‘scales’ ‘sna’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data        1.6Mb
    localdata   3.1Mb
Namespace in Imports field not imported from: ‘iterators’
  All declared Imports should be used.
File ‘pamr/libs/pamr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘smoothmest’
  All declared Imports should be used.
File ‘PanelCount/libs/PanelCount.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘M3C’
Namespace in Imports field not imported from: ‘survey’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘tibble’
  All declared Imports should be used.
File ‘parma/libs/parma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘parmigene/libs/parmigene.so’:
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’
File ‘parmigene/libs/parmigene.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
File ‘patchDVI/libs/patchDVI.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   1.2Mb
    doc    2.1Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘glue’ ‘logging’ ‘purrr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘KernSmooth’ ‘Mfuzz’ ‘SelectBoost’ ‘animation’ ‘c060’
  ‘cluster’ ‘gplots’ ‘grid’ ‘jetset’
  All declared Imports should be used.
File ‘pauwels2014/libs/pauwels2014.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    lib   9.9Mb
File ‘pbivnorm/libs/pbivnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.7Mb
File ‘PCA4TS/libs/PCA4TS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      3.5Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pander’
  All declared Imports should be used.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   7.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
installed size is 156.7Mb
  sub-directories of 1Mb or more:
    doc     2.7Mb
    libs  153.4Mb
File ‘PCICt/libs/PCICt.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    libs  33.0Mb
File ‘pdc/libs/pdc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘car’ ‘sandwich’
  All declared Imports should be used.
File ‘PDSCE/libs/PDSCE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
File ‘PedCNV/libs/PedCNV.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespace in Imports field not imported from: ‘lhs’
  All declared Imports should be used.
File ‘PenCoxFrail/libs/PenCoxFrail.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
File ‘peperr/libs/peperr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rms’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘SnowballC’ ‘cluster’ ‘graph’
  All declared Imports should be used.
File ‘pgee.mixed/libs/pgee.mixed.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   1.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data       2.3Mb
    examples   2.6Mb
File ‘phenmod/libs/phenmod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘jsonlite’ ‘memoise’
  All declared Imports should be used.
File ‘pheno/libs/pheno.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
Found the following significant warnings:
  phreeqcpp/transport.cpp:794:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/phreeqc.Rcheck/00install.out’ for details.
installed size is 42.4Mb
  sub-directories of 1Mb or more:
    libs  41.7Mb
Namespaces in Imports field not imported from:
  ‘gplots’ ‘phytools’
  All declared Imports should be used.
File ‘phyloland/libs/phyloland.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
File ‘PhyloMeasures/libs/PhyloMeasures.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘intergraph’
  All declared Imports should be used.
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  14.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Namespace in Imports field not imported from: ‘FrF2.catlg128’
  All declared Imports should be used.
File ‘Pijavski/libs/Pijavski.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
File ‘pirate/libs/pirate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘test-async.R’ [21s/27s]
  Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pkgcache)
  > 
  > test_check("pkgcache")
  ── 1. Error: load_primary_pkgs (@test-metadata-cache.R#191)  ───────────────────
  No metadata available
  Backtrace:
   1. pkgcache:::synchronise(get_private(cmc)$load_primary_pkgs(oneday()))
   2. get_private(cmc)$load_primary_pkgs(oneday())
   3. pkgcache:::cmc__load_primary_pkgs(self, private, max_age)
   4. private$update_replica_rds(alert = FALSE)
   5. pkgcache:::cmc__update_replica_rds(self, private, alert)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 305 | SKIPPED: 28 | WARNINGS: 2 | FAILED: 1 ]
  1. Error: load_primary_pkgs (@test-metadata-cache.R#191) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘stringi’
  All declared Imports should be used.
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
File ‘plac/libs/plac.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
File ‘planar/libs/planar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.7Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘RColorBrewer’ ‘arm’ ‘epiDisplay’ ‘foreign’ ‘gbm’
  ‘grid’ ‘lattice’ ‘latticeExtra’ ‘lme4’ ‘nnet’ ‘parallel’ ‘splines’
  ‘survey’ ‘twang’ ‘xtable’
  All declared Imports should be used.
File ‘plgp/libs/plgp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘PlackettLuce’ ‘StatRank’ ‘pmr’ ‘prefmod’ ‘rankdist’
  All declared Imports should be used.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   8.1Mb
File ‘pln/libs/pln.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.7Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘stats’
  All declared Imports should be used.
File ‘plugdensity/libs/plugdensity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
File ‘poilog/libs/poilog.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘car’ ‘lubridate’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: `data_frame()` is deprecated as of tibble 1.1.0.
See ‘/data/gannet/ripley/R/packages/tests-clang/poio.Rcheck/00install.out’ for details.
File ‘poisDoubleSamp/libs/poisDoubleSamp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘argonDash’ ‘argonR’ ‘colourpicker’ ‘ggplot2’ ‘grid’ ‘hexSticker’
  ‘png’ ‘shinyWidgets’
  All declared Imports should be used.
File ‘poLCA/libs/poLCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      6.4Mb
    data   4.0Mb
Namespace in Imports field not imported from: ‘combinat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘regtools’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Running ‘testthat.R’ [4m/12m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(portalr)
  > 
  > test_check("portalr")
  ── 1. Failure: default data path functions work if unset (@test-01-data-retrieva
  `m` does not match "Call `usethis::edit_r_environ\\(\\)` to open '.Renviron'".
  Actual value: ""
  
  ── 2. Failure: default data path functions work if unset (@test-01-data-retrieva
  `m` does not match "Store your data path with a line like:".
  Actual value: ""
  
  ── 3. Failure: default data path functions work if unset (@test-01-data-retrieva
  `m` does not match "PORTALR_DATA_PATH=".
  Actual value: ""
  
  ── 4. Failure: default data path functions work if unset (@test-01-data-retrieva
  `m` does not match "Make sure '.Renviron' ends with a newline!".
  Actual value: ""
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 194 | SKIPPED: 10 | WARNINGS: 4 | FAILED: 4 ]
  1. Failure: default data path functions work if unset (@test-01-data-retrieval.R#107) 
  2. Failure: default data path functions work if unset (@test-01-data-retrieval.R#108) 
  3. Failure: default data path functions work if unset (@test-01-data-retrieval.R#109) 
  4. Failure: default data path functions work if unset (@test-01-data-retrieval.R#110) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘StanHeaders’ ‘dplyr’ ‘ggplot2’ ‘gridExtra’ ‘rstan’ ‘tibble’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘ggthemes’ ‘memoise’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘shinyWidgets’
  All declared Imports should be used.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    doc  11.8Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
File ‘PPtree/libs/PPtree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lmtest’ ‘sandwich’
  All declared Imports should be used.
File ‘prclust/libs/prclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘class’ ‘forcats’ ‘irr’ ‘lpSolve’ ‘purrr’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.3Mb
Namespaces in Imports field not imported from:
  ‘TH.data’ ‘moonBook’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘ROCR’ ‘ada’ ‘colourpicker’ ‘corrplot’ ‘e1071’ ‘flexdashboard’
  ‘glmnet’ ‘kknn’ ‘neuralnet’ ‘randomForest’ ‘rattle’ ‘rpart’
  ‘shinyAce’ ‘shinyWidgets’ ‘shinydashboardPlus’ ‘shinyjs’ ‘tidyverse’
  ‘xgboost’ ‘zip’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘here’ ‘tidyr’
  All declared Imports should be used.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
Namespaces in Imports field not imported from:
  ‘datasets’ ‘dplyr’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘lubridate’
  All declared Imports should be used.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
File ‘PRIMAL/libs/PRIMAL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  16.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
File ‘ProbitSpatial/libs/ProbitSpatial.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘LaplacesDemon’ ‘epitools’ ‘rpivotTable’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc           8.8Mb
    htmlwidgets   2.6Mb
Namespaces in Imports field not imported from:
  ‘expm’ ‘mvtnorm’
  All declared Imports should be used.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    extdata   7.4Mb
    libs      6.3Mb
File ‘proj4/libs/proj4.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘distcrete’
  All declared Imports should be used.
Running ‘run-all.R’ [11s/23s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("ProjectTemplate")
  Loading required package: ProjectTemplate
  ── 1. Failure: Custom configuration is added to config (@test-add_config.R#12)  
  `load.project()` generated warnings:
  * 'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
  
  ✔ |  OK F W S | Context
  
  ⠏ |   0       | Example tests
  ✔ |   1       | Example tests
  
  ══ Results ═════════════════════════════════════════════════════════════════════
  OK:       1
  Failed:   0
  Warnings: 0
  Skipped:  0
  ✔ |  OK F W S | Context
  
  ⠏ |   0       | Example tests
  ✔ |   1       | Example tests
  
  ══ Results ═════════════════════════════════════════════════════════════════════
  OK:       1
  Failed:   0
  Warnings: 0
  Skipped:  0
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] TRUE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 852 | SKIPPED: 4 | WARNINGS: 281 | FAILED: 1 ]
  1. Failure: Custom configuration is added to config (@test-add_config.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   3.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    libs   3.1Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grDevices’
  All declared Imports should be used.
File ‘prototest/libs/prototest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   2.3Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘readr’
  All declared Imports should be used.
File ‘pRSR/libs/pRSR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘forecast’ ‘knitr’
  All declared Imports should be used.
File ‘pspearman/libs/pspearman.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 52.6Mb
  sub-directories of 1Mb or more:
    libs  51.5Mb
Namespace in Imports field not imported from: ‘pbv’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘methods’ ‘performance’ ‘tidyr’
  All declared Imports should be used.
File ‘ptest/libs/ptest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  pinpolyhedronA.cc:594:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  pinpolyhedronA.cc:1766:5: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/ptinpoly.Rcheck/00install.out’ for details.
File ‘ptinpoly/libs/ptinpoly.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    dict   5.1Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc        4.0Mb
    examples   2.6Mb
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘dplyr’
  All declared Imports should be used.
installed size is 52.1Mb
  sub-directories of 1Mb or more:
    libs  51.6Mb
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    libs  35.1Mb
File ‘pullword/libs/pullword.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘fractal’ ‘mgcv’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘hms’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘readr’ ‘tidyverse’
  All declared Imports should be used.
File ‘PWD/libs/PWD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    gui          1.7Mb
    staticdocs   3.4Mb
installed size is 93.1Mb
  sub-directories of 1Mb or more:
    libs  92.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
File ‘qrencoder/libs/qrencoder.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data  10.8Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘msm’
  All declared Imports should be used.
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
Error(s) in re-building vignettes:
--- re-building ‘qtlnet.Rnw’ using Sweave
Loading required package: qtl
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

Loading required package: sem
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:igraph’:

    normalize, path, union

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, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min


Attaching package: ‘graph’

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

    degree, edges, intersection

Loading required package: pcalg

Error: processing vignette 'qtlnet.Rnw' failed with diagnostics:
 chunk 2 
Error in igraph::graph.data.frame(edges, TRUE, vertices = vertices) : 
  Some vertex names in edge list are not listed in vertex data frame

--- failed re-building ‘qtlnet.Rnw’

SUMMARY: processing the following file failed:
  ‘qtlnet.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.8Mb
    doc       3.0Mb
    libs      1.6Mb
Namespace in Imports field not imported from: ‘MatrixModels’
  All declared Imports should be used.
File ‘QuACN/libs/QuACN.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs  13.6Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   6.8Mb
Found the following significant warnings:
  rf.c:454:1: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/quantregForest.Rcheck/00install.out’ for details.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   6.0Mb
File ‘QUIC/libs/QUIC.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘QUIC.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘QUIC.o’
File ‘QUIC/libs/QUIC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘gridExtra’ ‘knitr’
  All declared Imports should be used.
File ‘qVarSel/libs/qVarSel.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘qVarSelH.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘qVarSelH.o’
File ‘qVarSel/libs/qVarSel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘pracma’ ‘zoo’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lmerTest’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Package suggested but not available for checking: ‘batchelor’

Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    5.9Mb
    libs   1.2Mb
Namespaces in Imports field not imported from:
  ‘comat’ ‘rgdal’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.4Mb
File ‘RAD/libs/RAD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘hexbin’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘CGHbase’
  All declared Imports should be used.
installed size is 29.2Mb
  sub-directories of 1Mb or more:
    libs  28.3Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    api           3.2Mb
    htmlwidgets   7.1Mb
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘stringi’
  All declared Imports should be used.
File ‘randaes/libs/randaes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.2Mb
    libs   5.2Mb
Found the following significant warnings:
  rf.c:460:17: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/randomForest.Rcheck/00install.out’ for details.
File ‘randomUniformForest/libs/randomUniformForest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘curl’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘dplyr’ ‘jsonlite’ ‘rgbif’ ‘rgdal’ ‘rgeos’ ‘sp’ ‘spThin’
  ‘spatstat’
  All declared Imports should be used.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
File ‘RANKS/libs/RANKS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RJDBC’
  All declared Imports should be used.
File ‘rappdirs/libs/rappdirs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs  13.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.6Mb
File ‘RaschSampler/libs/RaschSampler.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs   7.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    etc    1.9Mb
    po     1.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is 33.1Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  30.1Mb
File ‘rBeta2009/libs/rBeta2009.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-clang/Rblpapi.Rcheck/00install.out’ for details.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    blp    7.1Mb
    libs   8.7Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
File ‘rbvs/libs/rbvs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    cont  25.8Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.0Mb
    po    2.4Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    corpora   7.6Mb
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    libs  27.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    include   6.0Mb
    libs      1.9Mb
File ‘RcppBDT/libs/RcppBDT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    lib    5.0Mb
    libs   1.6Mb
‘configure’: /bin/bash is not portable
  possible bashism in cleanup line 1 (brace expansion):
  rm -f src/*.{o,so}
  possible bashism in cleanup line 2 (brace expansion):
  rm -f src/cwb/cl/*.{a,o}
  possible bashism in cleanup line 4 (brace expansion):
  rm -f src/cwb/cqp/*.{a,o}
  possible bashism in cleanup line 8 (brace expansion):
  rm -r src/cwb/utils/*.{a,o}
File ‘RcppDL/libs/RcppDL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    include   7.9Mb
    libs     24.1Mb
File ‘RcppFaddeeva/libs/RcppFaddeeva.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 58.0Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib      42.9Mb
    libs     13.0Mb
File ‘RcppMLPACK/libs/RcppMLPACK.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    include   7.0Mb
    libs      2.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib       3.1Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    include   6.4Mb
    libs      5.5Mb
Registration problem:
  symbol ‘symbol’ in the local frame:
   .Call(symbol)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    jsonexamples   3.8Mb
    libs           1.8Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
File ‘RcppXts/libs/RcppXts.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’
  All declared Imports should be used.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
Found the following significant warnings:
  dist.cpp:19:33: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  dist.cpp:65:33: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  dist.cpp:111:36: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/rdist.Rcheck/00install.out’ for details.
Subdirectory ‘src’ contains:
  CLRApi.hpp CLRFactory.hpp CLRObjectRef.hpp Common.hpp OS.hpp
  RValue.hpp TcpClient.hpp
These are unlikely file names for src files.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
Error(s) in re-building vignettes:
--- re-building ‘Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd’ using rmarkdown
Loading required package: rJava
Loading required package: Rdroolsjars

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: 'purrr'

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

    set_names

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.thoughtworks.xstream.core.util.Fields (file:/tmp/RtmpL2nt6X/RLIBS_6f80434761fd/Rdroolsjars/java/xstream-1.4.9.jar) to field java.util.TreeMap.comparator
WARNING: Please consider reporting this to the maintainers of com.thoughtworks.xstream.core.util.Fields
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
Quitting from lines 183-187 (Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd) 
Error: processing vignette 'Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd' failed with diagnostics:
Assigned data `paste(seq(as.numeric(lowerRange), as.numeric(upperRange)), collapse = ",")` must be compatible with existing data.
ℹ Error occurred for column `Indices`.
✖ No common type for `value` <character> and `x` <double>.
--- failed re-building ‘Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd’

SUMMARY: processing the following file failed:
  ‘Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘digest’
  All declared Imports should be used.
File ‘Rdtq/libs/Rdtq.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(readroper)
  readroper package loaded.
  > 
  > test_check("readroper")
  ── 1. Error: First row of multicard dataset matches (@test-readroper.R#4)  ─────
  Must subset rows with a valid subscript vector.
  ℹ Logical subscripts must match the size of the indexed input.
  ✖ The input has size 1976 but the subscript `card_v` has size 2.
  Backtrace:
    1. readroper::read_rpr(...)
   16. vctrs:::stop_indicator_size(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: First row of multicard dataset matches (@test-readroper.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Note: found 1 marked Latin-1 string
  Note: found 1 marked UTF-8 string
  Note: found 7 strings marked as "bytes"
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
bestmods: no visible global function definition for ‘abline’
bestmods: no visible global function definition for ‘axis’
bestmods: no visible global function definition for ‘lines’
cic: no visible global function definition for ‘lsfit’
cic: no visible global function definition for ‘var’
cvic: no visible global function definition for ‘lsfit’
cvic: no visible global function definition for ‘lm’
eic: no visible global function definition for ‘lsfit’
eic: no visible global function definition for ‘lm’
ic.min: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘var’
xy: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘reams/R/xy.R’:
  assign(xname, X, env = .GlobalEnv)
  assign(yname, y, env = .GlobalEnv)
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   3.8Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.5Mb
Namespaces in Imports field not imported from:
  ‘DBI’ ‘readr’
  All declared Imports should be used.
Running ‘test-all.R’
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > # Modeled after the R6 testing structure: https://github.com/wch/R6/blob/master/tests/testthat.R
  > library(testthat)
  > library(REDCapR)
  > 
  > testthat::test_check("REDCapR")
  ── 1. Failure: validate_no_logical -concern dataset (@test-validate.R#36)  ─────
  ds$field_index not equal to 2.
  names for target but not for current
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 135 | SKIPPED: 79 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: validate_no_logical -concern dataset (@test-validate.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   6.0Mb
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs  17.6Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.7Mb
Namespaces in Imports field not imported from:
  ‘ROCR’ ‘colourpicker’ ‘corrplot’ ‘e1071’ ‘flexdashboard’ ‘gbm’
  ‘glmnet’ ‘kknn’ ‘neuralnet’ ‘rattle’ ‘rpart’ ‘shinyWidgets’
  ‘shinydashboardPlus’ ‘shinyjs’ ‘xgboost’ ‘zip’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘nnet’ ‘purrr’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘Rcplex’
File ‘relevent/libs/relevent.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gWidgetstcltk’
  All declared Imports should be used.
Running examples in ‘rematch2-Ex.R’ failed
The error most likely occurred in:

> ### Name: re_exec
> ### Title: Extract Data From First Regular Expression Match Into a Data
> ###   Frame
> ### Aliases: re_exec $.rematch_records $.rematch_allrecords
> 
> ### ** Examples
> 
> name_rex <- paste0(
+   "(?<first>[[:upper:]][[:lower:]]+) ",
+   "(?<last>[[:upper:]][[:lower:]]+)"
+ )
> notables <- c(
+   "  Ben Franklin and Jefferson Davis",
+   "\tMillard Fillmore"
+ )
> # Match first occurrence
> pos <- re_exec(notables, name_rex)
> pos
Error: Input must be a vector, not a `rematch_records` object.
Backtrace:
     █
  1. ├─(function (x, ...) ...
  2. ├─tibble:::print.tbl(x)
  3. │ ├─cli::cat_line(format(x, ..., n = n, width = width, n_extra = n_extra))
  4. │ │ └─base::paste0(..., collapse = "\n")
  5. │ ├─base::format(x, ..., n = n, width = width, n_extra = n_extra)
  6. │ └─tibble:::format.tbl(x, ..., n = n, width = width, n_extra = n_extra)
  7. │   └─tibble::trunc_mat(x, n = n, width = width, n_extra = n_extra)
  8. │     ├─base::as.data.frame(head(x, n))
  9. │     ├─utils::head(x, n)
 10. │     └─utils:::head.data.frame(x, n)
 11. │       ├─base::do.call("[", args)
 12. │       ├─x[1:2, , drop = FALSE]
 13. │       └─tibble:::`[.tbl_df`(x, 1:2, , drop = FALSE)
 14. │         └─tibble:::tbl_subset_row(xo, i = i, i_arg)
 15. │           └─base::lapply(unclass(x), vec_slice, i = i)
 16. │             └─vctrs:::FUN(X[[i]
Execution halted
File ‘remMap/libs/remMap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs   2.4Mb
File ‘ReorderCluster/libs/ReorderCluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
File ‘repolr/libs/repolr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.7Mb
Found the following significant warnings:
  regalg.cpp:215:10: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
  regalg.cpp:454:10: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/resemble.Rcheck/00install.out’ for details.
File ‘resemble/libs/resemble.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs      4.2Mb
    swagger   1.4Mb
Namespace in Imports field not imported from: ‘Rserve’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.4Mb
File ‘retimes/libs/retimes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RTriangle’
  All declared Imports should be used.
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    libs  24.6Mb
installed size is 65.0Mb
  sub-directories of 1Mb or more:
    libs  63.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   1.9Mb
Error(s) in re-building vignettes:
--- re-building ‘RFmerge-RainfallExample-minimal.Rmd’ using rmarkdown

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Linking to GEOS 3.7.1, GDAL 2.3.2, PROJ 5.2.0
Loading required package: sp
rgdal: version: 1.4-8, (SVN revision 845)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.3.2, released 2018/09/21
 Path to GDAL shared files: /usr/share/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 5.2.0, September 15th, 2018, [PJ_VERSION: 520]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.4-1 
(C) 2019 M. Zambrano-Bigiarini and Oscar M. Baez-Villanueva (GPL >=3 license)
Type 'citation('RFmerge')' to see how to cite this package
Quitting from lines 268-274 (RFmerge-RainfallExample-minimal.Rmd) 
Error: processing vignette 'RFmerge-RainfallExample-minimal.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘RFmerge-RainfallExample-minimal.Rmd’

SUMMARY: processing the following file failed:
  ‘RFmerge-RainfallExample-minimal.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    java   5.3Mb
Namespaces in Imports field not imported from:
  ‘prob’ ‘titanic’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       2.2Mb
    extdata   2.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   2.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      2.1Mb
Namespaces in Imports field not imported from:
  ‘leaflet’ ‘pals’ ‘raster’ ‘sp’
  All declared Imports should be used.
Running examples in ‘RGISTools-Ex.R’ failed
The error most likely occurred in:

> ### Name: varEVI
> ### Title: Calculate the enhanced vegetation index (EVI)
> ### Aliases: varEVI
> 
> ### ** Examples
> 
> # path to the cropped and cutted MODIS images for the region of Navarre
> wdir <- system.file("ExNavarreVar", package = "RGISTools")
> # list all the tif files
> files.mod <- list.files(wdir, pattern = "\\.tif$", recursive = TRUE, full.names = TRUE)
> # print the MOD09 bands
> getRGISToolsOpt("MOD09BANDS")
           red            nir           blue          green          tirs1 
       "B01_1"        "B02_1"        "B03_1"        "B04_1"        "B05_1" 
         swir1          swir2        quality          cloud 
       "B06_1"        "B07_1" "_state_1km_1"          "CLD" 
> scale.factor <- 0.0001
> 
> # select the red, blue and nir bands
> img.mod.red <- raster(files.mod[1]) * scale.factor
Error in .rasterObjectFromFile(x, band = band, objecttype = "RasterLayer",  : 
  Cannot create RasterLayer object from this file; perhaps you need to install rgdal first
Calls: raster -> raster -> .local -> .rasterObjectFromFile
Execution halted
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc     3.7Mb
    fonts   1.5Mb
    libs    2.7Mb
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.6Mb
    libs   9.1Mb
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’
File ‘RGtk2/libs/RGtk2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc          10.2Mb
    htmlwidgets   1.2Mb
File ‘RI2by2/libs/RI2by2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
File ‘Rip46/libs/Rip46.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
File ‘rIsing/libs/rIsing.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [6s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(riskclustr)
  > 
  > test_check("riskclustr")
  ── 1. Error: optimal_kmeans_d prints message if no seed is set (@test-optimal_km
  `i` must have one dimension, not 2.
  Backtrace:
    1. testthat::expect_message(...)
    6. riskclustr::optimal_kmeans_d(...)
    7. base::lapply(...)
    8. riskclustr:::FUN(X[[i]], ...)
    9. riskclustr::d(label = "cls", M = M, factors = factors, data = temp)
   12. tibble:::`[.tbl_df`(data, data[, label] == 0, )
   13. tibble:::tbl_subset_row(xo, i = i, i_arg)
   14. tibble:::vectbl_as_row_index(i, x, i_arg)
   15. tibble:::vectbl_as_row_location(i, nr, i_arg, assign)
   22. vctrs::vec_as_location(i, n, arg = as_label(i_arg))
  
  ── 2. Error: optimal_kmeans_d returns expected optimal_d value (@test-optimal_km
  `i` must have one dimension, not 2.
  Backtrace:
    1. testthat::expect_equal(...)
    4. riskclustr::optimal_kmeans_d(...)
    5. base::lapply(...)
    6. riskclustr:::FUN(X[[i]], ...)
    7. riskclustr::d(label = "cls", M = M, factors = factors, data = temp)
   10. tibble:::`[.tbl_df`(data, data[, label] == 0, )
   11. tibble:::tbl_subset_row(xo, i = i, i_arg)
   12. tibble:::vectbl_as_row_index(i, x, i_arg)
   13. tibble:::vectbl_as_row_location(i, nr, i_arg, assign)
   20. vctrs::vec_as_location(i, n, arg = as_label(i_arg))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 26 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 2 ]
  1. Error: optimal_kmeans_d prints message if no seed is set (@test-optimal_kmeans_d.R#49) 
  2. Error: optimal_kmeans_d returns expected optimal_d value (@test-optimal_kmeans_d.R#65) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘calculate_d.Rmd’ using rmarkdown
--- finished re-building ‘calculate_d.Rmd’

--- re-building ‘contribute.Rmd’ using rmarkdown
--- finished re-building ‘contribute.Rmd’

--- re-building ‘eh_test.Rmd’ using rmarkdown
--- finished re-building ‘eh_test.Rmd’

--- re-building ‘factor_pvalue.Rmd’ using rmarkdown

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

--- finished re-building ‘factor_pvalue.Rmd’

--- re-building ‘optimal_d.Rmd’ using rmarkdown
Quitting from lines 36-46 (optimal_d.Rmd) 
Error: processing vignette 'optimal_d.Rmd' failed with diagnostics:
`i` must have one dimension, not 2.
--- failed re-building ‘optimal_d.Rmd’

SUMMARY: processing the following file failed:
  ‘optimal_d.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 24.5Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  22.9Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/rJava.Rcheck/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.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   4.4Mb
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    exe  23.8Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘arules’ ‘pmml’ ‘rJava’
  All declared Imports should be used.
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
File ‘rkvo/libs/rkvo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 59.3Mb
  sub-directories of 1Mb or more:
    libs  58.6Mb
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    libs  25.8Mb
File ‘rlm/libs/rlm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RCarb’ ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Running examples in ‘RmarineHeatWaves-Ex.R’ failed
The error most likely occurred in:

> ### Name: detect
> ### Title: Detect heatwaves and cold-spells.
> ### Aliases: detect
> 
> ### ** Examples
> 
> ts_dat <- make_whole(sst_WA)
> res <- detect(ts_dat, climatology_start = "1983-01-01",
+               climatology_end = "2012-12-31")
Error: Assigned data `zoo::na.approx(tDat[59:61, no_NA], maxgap = 1, na.rm = TRUE)` must be compatible with existing data.
ℹ Error occurred for column `doy`.
✖ Can't cast <double[,31]> to <double>.
Can not decrease dimensions.
Backtrace:
    █
 1. └─RmarineHeatWaves::detect(...)
 2.   ├─base::`[<-`(...)
 3.   └─tibble:::`[<-.tbl_df`(...)
 4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 5.       └─tibble:::tbl_subassign_row(xj, i, value, value_arg)
 6.         └─base::tryCatch(...)
 7.           └─base:::tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)
Execution halted
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    rmd   8.3Mb
Found the following files/directories:
  ‘dipper.inp’ ‘mark001.inp’ ‘mark001.out’ ‘mark001.res’ ‘mark001.vcv’
  ‘mark002.inp’ ‘mark002.out’ ‘mark002.res’ ‘mark002.vcv’ ‘mark003.inp’
  ‘mark003.out’ ‘mark003.res’ ‘mark003.vcv’ ‘mark004.inp’ ‘mark004.out’
  ‘mark004.res’ ‘mark004.vcv’ ‘mark005.inp’ ‘mark005.out’ ‘mark005.res’
  ‘mark005.vcv’ ‘mark006.inp’ ‘mark006.out’ ‘mark006.res’ ‘mark006.vcv’
  ‘mark007.inp’ ‘mark007.out’ ‘mark007.res’ ‘mark007.vcv’ ‘mark008.inp’
  ‘mark008.out’ ‘mark008.res’ ‘mark008.vcv’ ‘mark009.inp’ ‘mark009.out’
  ‘mark009.res’ ‘mark009.vcv’ ‘mark010.inp’ ‘mark010.out’ ‘mark010.res’
  ‘mark010.vcv’ ‘mark010V.tmp’ ‘mark010X.tmp’ ‘mark010Y.tmp’
  ‘mark011.inp’ ‘mark011.out’ ‘mark011.res’ ‘mark011.vcv’ ‘mark012.inp’
  ‘mark012.out’ ‘mark012.res’ ‘mark012.vcv’ ‘mark013.inp’ ‘mark013.out’
  ‘mark013.res’ ‘mark013.vcv’
installed size is 60.7Mb
  sub-directories of 1Mb or more:
    libs  59.9Mb
Namespaces in Imports field not imported from:
  ‘blogdown’ ‘bookdown’ ‘bookdownplus’ ‘citr’ ‘pagedown’ ‘rticles’
  ‘tinytex’ ‘xaringan’
  All declared Imports should be used.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   7.0Mb
installed size is 40.5Mb
  sub-directories of 1Mb or more:
    libs  39.6Mb
installed size is 34.8Mb
  sub-directories of 1Mb or more:
    libs  34.6Mb
File ‘RMKdiscrete/libs/RMKdiscrete.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘statmod’
  All declared Imports should be used.
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
Running examples in ‘rmutil-Ex.R’ failed
The error most likely occurred in:

> ### Name: tvctomat
> ### Title: Create a Time-varying, Intra-individual Covariate (tvcov) Object
> ### Aliases: tvctomat
> ### Keywords: manip
> 
> ### ** Examples
> 
> z <- matrix(rpois(20,5),ncol=5)
> print(tvc <- tvctomat(z, units="days"))
           
Names: z   
Units: days
Number of individuals:                4 
Number of observations:               20 
Number of observations per individual:
 5 5 5 5 
> covariates(tvc)
 [1]  4  3  6  6  6  4  8  2  4 11  5  9  3  7  4  8  6  3  5  7
> names(tvc)
[1] "z"
> v <- data.frame(matrix(rep(c("a","b","c","d","e"),4),ncol=5))
> print(tvc2 <- tvctomat(v, oldtvc=tvc, units=NA))
                
Names: z    v   
Units: days <NA>
Number of individuals:                4 
Number of observations:               20 
Number of observations per individual:
 5 5 5 5 
> covariates(tvc2)
    z v
1   4 a
2   3 e
3   6 d
4   6 c
5   6 b
6   4 b
7   8 a
8   2 e
9   4 d
10 11 c
11  5 c
12  9 b
13  3 a
14  7 e
15  4 d
16  8 d
17  6 c
18  3 b
19  5 a
20  7 e
> print(tvc3 <- tvctomat(v, oldtvc=tvc, dataframe=FALSE, units=NA))
                               
Names: z    vb   vc   vd   ve  
Units: days <NA> <NA> <NA> <NA>
Number of individuals:                4 
Number of observations:               20 
Number of observations per individual:
 5 5 5 5 
> covariates(tvc3)
    z vb vc vd ve
1   4  0  0  0  0
2   3  0  0  0  1
3   6  0  0  1  0
4   6  0  1  0  0
5   6  1  0  0  0
6   4  1  0  0  0
7   8  0  0  0  0
8   2  0  0  0  1
9   4  0  0  1  0
10 11  0  1  0  0
11  5  0  1  0  0
12  9  1  0  0  0
13  3  0  0  0  0
14  7  0  0  0  1
15  4  0  0  1  0
16  8  0  0  1  0
17  6  0  1  0  0
18  3  1  0  0  0
19  5  0  0  0  0
20  7  0  0  0  1
> print(tvc4 <- tvctomat(tvc2, interaction=c("z","v")))
Error in dimnames(x) <- dn : 
  length of 'dimnames' [2] not equal to array extent
Calls: print -> tvctomat -> colnames<-
Execution halted
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    libs  23.3Mb
File ‘rnetcarto/libs/rnetcarto.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
File ‘rngSetSeed/libs/rngSetSeed.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rngwell19937/libs/rngwell19937.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doxygen   1.6Mb
    libs      3.6Mb
installed size is 92.7Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     90.5Mb
Namespace in Imports field not imported from: ‘impute’
  All declared Imports should be used.
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
Namespaces in Imports field not imported from:
  ‘abind’ ‘foreach’
  All declared Imports should be used.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R  11.2Mb
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  16.2Mb
File ‘robcp/libs/robcp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘DEoptimR’ ‘DT’ ‘PerformanceAnalytics’ ‘ggplot2’ ‘graphics’
  ‘gridExtra’ ‘methods’ ‘shinyjs’ ‘utils’ ‘xts’
  All declared Imports should be used.
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
File ‘robustETM/libs/robustETM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    libs  23.5Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 34.8Mb
  sub-directories of 1Mb or more:
    libs  33.7Mb
File ‘robustloggamma/libs/robustloggamma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   2.7Mb
Namespace in Imports field not imported from: ‘matrixcalc’
  All declared Imports should be used.
File ‘Rook/libs/Rook.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 25.4Mb
  sub-directories of 1Mb or more:
    libs  25.3Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘methods’
  All declared Imports should be used.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.7Mb
    libs   6.3Mb
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘utils’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    libs    2.5Mb
    tests   1.3Mb
File ‘rpartitions/libs/rpartitions.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    libs  21.7Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   5.5Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘testthat’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Namespaces in Imports field not imported from:
  ‘ape’ ‘igraph’
  All declared Imports should be used.
File ‘rPython/libs/rPython.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘NatureSounds’
  All declared Imports should be used.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    extdata  12.8Mb
File ‘rredis/libs/rredis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  rf.c:485:1: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/RRF.Rcheck/00install.out’ for details.
File ‘rr/libs/rr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

> ### Name: VeterinaryData
> ### Title: Symbolic interval data example
> ### Aliases: VeterinaryData
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(VeterinaryData)
> VeterinaryData
Error in get(x, envir = ns, inherits = FALSE) : 
  object 'warningc' not found
Calls: <Anonymous> ... do.call -> [ -> [.symbolic_tbl -> getFromNamespace -> get
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 40-42 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
object 'warningc' not found
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
File ‘rsdepth/libs/rsdepth.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘binman’ ‘httr’
  All declared Imports should be used.
Found the following significant warnings:
  Rserv.c:2150:17: warning: 'RSA_generate_key' is deprecated [-Wdeprecated-declarations]
  oc.c:47:33: warning: 'RAND_pseudo_bytes' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/Rserve.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor 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.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
File ‘RSKC/libs/RSKC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘miniUI’ ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘methods’ ‘tcltk’ ‘tools’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
Namespace in Imports field not imported from: ‘h2o’
  All declared Imports should be used.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 47.2Mb
  sub-directories of 1Mb or more:
    libs  46.5Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
installed size is 217.6Mb
  sub-directories of 1Mb or more:
    R       1.6Mb
    doc     4.5Mb
    libs  210.9Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
installed size is 27.8Mb
  sub-directories of 1Mb or more:
    libs  27.4Mb
installed size is 191.6Mb
  sub-directories of 1Mb or more:
    libs  188.8Mb
installed size is 102.2Mb
  sub-directories of 1Mb or more:
    libs  100.8Mb
Namespace in Imports field not imported from: ‘loo’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  14.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
File ‘RSvgDevice/libs/RSvgDevice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    Lib  11.9Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘bookdown’ ‘ggplot2’ ‘knitr’ ‘rmarkdown’ ‘xfun’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘stats’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       2.9Mb
    projects   2.8Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Namespace in Imports field not imported from: ‘quantmod’
  All declared Imports should be used.
Found the following significant warnings:
  getFunctions.cpp:90:16: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/RTransProb.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘memoise’ ‘tidyr’
  All declared Imports should be used.
installed size is 30.7Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  21.9Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.4Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   8.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
Namespace in Imports field not imported from: ‘RGtk2’
  All declared Imports should be used.
installed size is 58.6Mb
  sub-directories of 1Mb or more:
    libs  57.8Mb
File ‘rvgtest/libs/rvgtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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   5.3Mb
installed size is 57.7Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs     53.4Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/RVowpalWabbit.Rcheck/00install.out’ for details.
Running examples in ‘rwars-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_all_planets
> ### Title: Retrieve Data about Every DB Entry in a Class
> ### Aliases: all_entries get_all_films get_all_people get_all_planets
> ###   get_all_species get_all_starships get_all_vehicles
> 
> ### ** Examples
> 
> #Retrieve all planets, parsing
> planets <- get_all_planets(parse_result = TRUE)
Error in query("/planets/", ...) : Not Found (HTTP 404).
Calls: get_all_planets -> query -> stop_for_status
Execution halted
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
File ‘rwfec/libs/rwfec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  qwiener.c:60:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  qwiener.c:69:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/RWiener.Rcheck/00install.out’ for details.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs    8.7Mb
    yacas   1.5Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs    9.4Mb
    yacas   1.6Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
possible bashism in configure line 34 ($(OS|MACH)TYPE):
    case "$OSTYPE" in "darwin"*)
  possible bashism in configure line 40 (should be '.', not 'source'):
      source autobrew
Namespace in Imports field not imported from: ‘spanel’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘mgcv’
  All declared Imports should be used.
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/SafeBayes.Rcheck/00install.out’ for details.
File ‘SafeBayes/libs/SafeBayes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘shinybusy’
  All declared Imports should be used.
File ‘SALES/libs/SALES.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs  13.2Mb
Namespaces in Imports field not imported from:
  ‘gdistance’ ‘methods’
  All declared Imports should be used.
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  16.5Mb
File ‘sampling/libs/sampling.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   3.8Mb
File ‘sanitizers/libs/sanitizers.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘purrr’ ‘tidyr’
  All declared Imports should be used.
Running examples in ‘SanzCircos-Ex.R’ failed
The error most likely occurred in:

> ### Name: make_circos_links
> ### Title: make_circos_links
> ### Aliases: make_circos_links
> 
> ### ** Examples
> 
> 
> links_df <- data.frame(chrom = c(rep("chr1", 5), rep("chr2", 5)),
+ band = c(rep("band1", 3), rep("band2", 2), "band1", rep("band2", 4)),
+ link = c(1, 2, 3, 1, 2, 1, 1, 3, 4, 5),
+ start = c(1, 3, 5, 10, 35, 1, 5, 8, 13, 15),
+ end = c(3, 5, 10, 35, 39, 5, 8, 13, 15, 21))
> 
> links <- make_circos_links(links_df, "chrom", "band", "link", "start", "end", status = TRUE)
Warning: `as.tibble()` is deprecated as of tibble 2.0.0.
Please use `as_tibble()` instead.
The signature and semantics have changed, see `?as_tibble`.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Error: Assigned data `as.character(df[[chromosome_grouping]][i])` must be compatible with existing data.
ℹ Error occurred for column `V2`.
✖ Lossy cast from `value` <character> to `x` <logical>.
* Locations: 1.
Backtrace:
     █
  1. └─SanzCircos::make_circos_links(...)
  2.   ├─dplyr::bind_rows(...)
  3.   │ ├─dplyr:::flatten_bindable(dots_values(...))
  4.   │ └─rlang::dots_values(...)
  5.   └─pbapply::pblapply(...)
  6.     └─base::lapply(X, FUN, ...)
  7.       └─SanzCircos:::FUN(X[[i]], ...)
  8.         ├─base::`[<-`(`*tmp*`, 1, 2, value = "chr1")
  9.         └─tibble:::`[<-.tbl_df`(`*tmp*`, 1, 2, value = "chr1")
 10.           └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 11.             └─tibble:::tbl_subassign_row(xj, i, value, value_arg)
 12.               └─base::tryCatch(...)
 13.                 └─base:::tryCatchList(expr, classes, parentenv, handlers)
 14.                   └
Execution halted
File ‘sapa/libs/sapa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 63.0Mb
  sub-directories of 1Mb or more:
    extdata  62.6Mb
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.0Mb
File ‘saturnin/libs/saturnin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
Namespace in Imports field not imported from: ‘pvclust’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘methods’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
File ‘scar/libs/scar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
File ‘SCEPtERbinary/libs/SCEPtERbinary.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
File ‘SCEPtER/libs/SCEPtER.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘spData’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘stringi’ ‘stringr’ ‘tibble’ ‘tidyr’ ‘tidytext’
  All declared Imports should be used.
File ‘scio/libs/scio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
File ‘scout/libs/scout.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.2Mb
Namespace in Imports field not imported from: 'lpSolveAPI'
  All declared Imports should be used.
File ‘SDDE/libs/SDDE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gbm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘covr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’ ‘tidyr’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R   7.1Mb
File ‘SearchTrees/libs/SearchTrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

> ### Name: add_travis_user
> ### Title: Add a user via their Travis repo.
> ### Aliases: add_travis_user
> 
> ### ** Examples
> 
> vault <- file.path(tempdir(), ".vault")
> create_vault(vault)
> 
> add_travis_user("gaborcsardi/secret", vault = vault)
Error in open.connection(con, "rb") : HTTP error 404.
Calls: add_travis_user ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(secret)
  > 
  > test_check("secret")
  ── 1. Failure: update a secret, deleted user has no access (@test-6-issues.R#67)
  `openssl::aes_cbc_decrypt(secret, aes)` did not throw an error.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 73 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: update a secret, deleted user has no access (@test-6-issues.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  17.6Mb
Namespaces in Imports field not imported from:
  ‘ForeCA’ ‘Mcomp’ ‘repmis’
  All declared Imports should be used.
File ‘segmag/libs/segmag.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking: 'flowMerge', 'flowClust'
Packages unavailable to check Rd xrefs: ‘flowClust’, ‘flowMerge’
Found the following significant warnings:
  BinNegative.cpp:108:5: warning: assigning field to itself [-Wself-assign-field]
See ‘/data/gannet/ripley/R/packages/tests-clang/Segmentor3IsBack.Rcheck/00install.out’ for details.
File ‘Segmentor3IsBack/libs/Segmentor3IsBack.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘cluster’ ‘factoextra’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘FD’
  All declared Imports should be used.
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’
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 predict runif splinefun uniroot
Consider adding
  importFrom("stats", "dbeta", "dbinom", "integrate", "pbeta", "predict",
             "runif", "splinefun", "uniroot")
to your NAMESPACE file.
File ‘SEL/libs/SEL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lavaan’ ‘psych’ ‘semPlot’ ‘semTools’ ‘shinyAce’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
Namespaces in Imports field not imported from:
  ‘htmlTable’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘SemNetCleaner’ ‘grid’ ‘purrr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘expm’ ‘matrixStats’ ‘matrixcalc’
  All declared Imports should be used.
File ‘semver/libs/semver.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sensitivityPStrat/libs/sensitivityPStrat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   5.3Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs  15.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Package suggested but not available for checking: ‘muscle’
File ‘seqMeta/libs/seqMeta.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 23.2Mb
  sub-directories of 1Mb or more:
    libs  21.8Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
    libs   1.1Mb
File ‘sequences/libs/sequences.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
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.
Packages suggested but not available for checking:
  'loomR', 'SDMTools', 'MAST', 'monocle'

Imports includes 36 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   8.1Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    doc     11.9Mb
    libs    10.2Mb
    sqlite   1.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
File ‘sgeostat/libs/sgeostat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.4Mb
Namespaces in Imports field not imported from:
  ‘parallel’ ‘plyr’
  All declared Imports should be used.
File ‘sharpData/libs/sharpData.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
Namespace in Imports field not imported from: ‘brms’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinydashboard’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘VGAM’ ‘data.table’ ‘ggdendro’ ‘gridExtra’ ‘knitr’
  ‘latticeExtra’ ‘msm’ ‘plotly’ ‘shinyBS’ ‘shinydashboard’ ‘xtable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘getPass’ ‘svglite’ ‘websocket’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘shiny’ ‘shinyjs’
  All declared Imports should be used.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    www   8.3Mb
Namespaces in Imports field not imported from:
  ‘CARE1’ ‘LCMCR’ ‘coda’ ‘conting’ ‘dga’ ‘future’ ‘ggplot2’ ‘ipc’
  ‘promises’ ‘reshape’ ‘shinycssloaders’ ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘knitr’ ‘plotly’
  All declared Imports should be used.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    www   8.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
File ‘siar/libs/siar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘coda’ ‘ellipse’ ‘viridis’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘animate.Rmd’ using rmarkdown
--- finished re-building ‘animate.Rmd’

--- re-building ‘buttons.Rmd’ using rmarkdown
--- finished re-building ‘buttons.Rmd’

--- re-building ‘cluster.Rmd’ using rmarkdown
--- finished re-building ‘cluster.Rmd’

--- re-building ‘dynamic.Rmd’ using rmarkdown
Quitting from lines 27-45 (dynamic.Rmd) 
Error: processing vignette 'dynamic.Rmd' failed with diagnostics:
Assigned data `runif(15, 500, 750)` must be compatible with existing data.
✖ Existing data has 75 rows.
✖ Assigned data has 15 rows.
ℹ Only vectors of size 1 are recycled.
--- failed re-building ‘dynamic.Rmd’

--- re-building ‘formats.Rmd’ using rmarkdown
--- finished re-building ‘formats.Rmd’

--- re-building ‘get_started.Rmd’ using rmarkdown
--- finished re-building ‘get_started.Rmd’

--- re-building ‘layout.Rmd’ using rmarkdown
--- finished re-building ‘layout.Rmd’

--- re-building ‘plugins.Rmd’ using rmarkdown
--- finished re-building ‘plugins.Rmd’

--- re-building ‘settings.Rmd’ using rmarkdown
--- finished re-building ‘settings.Rmd’

--- re-building ‘shiny.Rmd’ using rmarkdown
--- finished re-building ‘shiny.Rmd’

--- re-building ‘talkcross.Rmd’ using rmarkdown
--- finished re-building ‘talkcross.Rmd’

SUMMARY: processing the following file failed:
  ‘dynamic.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'chromVAR', 'TFBSTools', 'motifmatchr', 'EnsDb.Hsapiens.v75',
  'JASPAR2018'

Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Packages unavailable to check Rd xrefs: ‘TFBSTools’, ‘motifmatchr’, ‘chromVAR’
File ‘signal/libs/signal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.2Mb
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘MASS’ ‘class’ ‘cluster’ ‘lattice’ ‘nnet’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘car’ ‘ggplot2’ ‘magrittr’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grid’
  All declared Imports should be used.
File ‘simFrame/libs/simFrame.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘future’ ‘magrittr’ ‘purrr’ ‘rlang’ ‘utils’
  All declared Imports should be used.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  13.2Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘plotly’ ‘readr’ ‘rmarkdown’ ‘shinycssloaders’
  All declared Imports should be used.
File ‘simplexreg/libs/simplexreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
File ‘SimReg/libs/SimReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [6s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(simrel)
  > 
  > test_check("simrel")
  ── 1. Error: Prepare Design (@test-utils.R#44)  ────────────────────────────────
  Can't join on 'q' x 'q' because of incompatible types (list / list)
  Backtrace:
   1. testthat::expect_identical(prepare_design(opts), dgn)
   3. testthat:::compare.default(act$val, exp$val)
   5. dplyr:::all.equal.tbl_df(x, y, ...)
   6. dplyr:::equal_data_frame(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 169 | SKIPPED: 21 | WARNINGS: 3 | FAILED: 1 ]
  1. Error: Prepare Design (@test-utils.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  23.5Mb
Error(s) in re-building vignettes:
--- re-building ‘SimVitD.Rnw’ using Sweave
Error: processing vignette 'SimVitD.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'SimVitD.tex' failed.
LaTeX errors:
! LaTeX Error: File `tkz-graph.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.24 \usetikzlibrary
                    {shapes.geometric}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘SimVitD.Rnw’

SUMMARY: processing the following file failed:
  ‘SimVitD.Rnw’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘pracma’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘psych’ ‘stringr’
  All declared Imports should be used.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   8.5Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
File ‘skda/libs/skda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘car’ ‘het.test’ ‘lmtest’ ‘lubridate’ ‘magrittr’ ‘tibble’ ‘tseries’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.9Mb
File ‘skm/libs/skm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 35.0Mb
  sub-directories of 1Mb or more:
    libs  33.4Mb
File ‘sld/libs/sld.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
File ‘SLHD/libs/SLHD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘viridisLite’
  All declared Imports should be used.
File ‘SLOPE/libs/SLOPE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘slp/libs/slp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 15 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘Amelia’ ‘Boruta’ ‘DMwR’ ‘MVN’ ‘NoiseFiltersR’ ‘VIM’ ‘adaptiveGPCA’
  ‘class’ ‘clusterSim’ ‘denoiseR’ ‘discretization’ ‘imbalance’ ‘lle’
  ‘missForest’ ‘missMDA’ ‘outliers’ ‘unbalanced’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
Imports includes 36 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.

Requires orphaned package: ‘clues’
File ‘SMC/libs/SMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘smds/libs/smds.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs  11.6Mb
Found the following significant warnings:
  ./Scythe_IDE.cpp:70:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:107:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:108:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:109:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:147:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:148:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:149:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:189:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:211:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:212:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:262:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:265:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:266:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/data/gannet/ripley/R/packages/tests-clang/smoothSurv.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘ggplot2’
  All declared Imports should be used.
File ‘snipEM/libs/snipEM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘snnR/libs/snnR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      3.0Mb
File ‘snpStatsWriter/libs/snpStatsWriter.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘raster’ ‘rlang’ ‘sp’ ‘usethis’
  All declared Imports should be used.
File ‘SocialNetworks/libs/SocialNetworks.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SoDA/libs/SoDA.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘softImpute/libs/softImpute.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data  11.7Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘nnet’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘AGread’ ‘caret’
  All declared Imports should be used.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.6Mb
    libs   6.6Mb
File ‘som/libs/som.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SoundexBR/libs/SoundexBR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
File ‘SpaCCr/libs/SpaCCr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘space/libs/space.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘rstudioapi’
  All declared Imports should be used.
installed size is 36.5Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    libs  34.0Mb
Imports includes 28 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
File ‘sparcl/libs/sparcl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SparseFactorAnalysis/libs/SparseFactorAnalysis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
File ‘sparseLTSEigen/libs/sparseLTSEigen.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sparsereg/libs/sparsereg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sparseSEM/libs/sparseSEM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SparseTSCGM/libs/SparseTSCGM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
File ‘spate/libs/spate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘irlba’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘SpatialEpi’ ‘dplyr’ ‘dygraphs’ ‘ggplot2’
  ‘htmlwidgets’ ‘knitr’ ‘leaflet’ ‘mapproj’ ‘maptools’ ‘rgdal’ ‘rgeos’
  ‘rmarkdown’ ‘shinyjs’ ‘spdep’ ‘xts’
  All declared Imports should be used.
File ‘spatialfil/libs/spatialfil.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [8s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(SpatialKDE)
  > 
  > test_check("SpatialKDE")
  ── 1. Error: (unknown) (@test-kde.R#29)  ───────────────────────────────────────
  package 'rgdal' is not available
  Backtrace:
   1. base::suppressWarnings(...)
   3. raster::projectRaster(test_raster, crs = "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")
   4. raster:::.requireRgdal()
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 14 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test-kde.R#29) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.2Mb
Note: found 25 marked Latin-1 strings
  Note: found 658 marked UTF-8 strings
Running examples in ‘spatial.tools-Ex.R’ failed
The error most likely occurred in:

> ### Name: tahoe_highrez_training
> ### Title: Point and polygon files for use with spatial.tools
> ### Aliases: tahoe_highrez_training
> ### Keywords: data
> 
> ### ** Examples
> 
> library("raster")
Loading required package: sp
> library("rgdal")
rgdal: version: 1.4-8, (SVN revision 845)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.3.2, released 2018/09/21
 Path to GDAL shared files: /usr/share/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 5.2.0, September 15th, 2018, [PJ_VERSION: 520]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.4-1 
> tahoe_highrez_training_polygons <- readOGR(
+ 	dsn=system.file("external", package="spatial.tools"),layer="tahoe_highrez_training")
OGR data source with driver: ESRI Shapefile 
Source: "/data/gannet/ripley/R/packages/tests-clang/spatial.tools.Rcheck/spatial.tools/external", layer: "tahoe_highrez_training"
with 8 features
It has 2 fields
> spplot(tahoe_highrez_training_polygons,zcol="Class")
Warning in extend.limits(range(as.numeric(z), finite = TRUE)) :
  NAs introduced by coercion
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 seq.default(zrng[1], zrng[2], length.out = cuts + 2) : 
  'from' must be a finite number
Calls: spplot ... <Anonymous> -> levelplot.formula -> seq -> seq.default
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is 33.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  31.8Mb
File ‘SpaTimeClus/libs/SpaTimeClus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘spatstat.Knet/libs/spatstat.Knet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    R      5.3Mb
    doc    4.9Mb
    help   5.3Mb
    libs   2.1Mb
installed size is 35.7Mb
  sub-directories of 1Mb or more:
    libs  34.8Mb
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    libs  11.7Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
File ‘spcr/libs/spcr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data     2.2Mb
    shapes   3.2Mb
File ‘SPECIES/libs/SPECIES.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   2.9Mb
Namespace in Imports field not imported from: ‘pdftools’
  All declared Imports should be used.
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nr' to 'nrow'
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nc' to 'ncol'
spe: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘spe/libs/spe.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’
  All declared Imports should be used.
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    libs  22.7Mb
File ‘spikeslab/libs/spikeslab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Namespaces in Imports field not imported from:
  ‘GGally’ ‘tibble’ ‘webshot’
  All declared Imports should be used.
File ‘splus2R/libs/splus2R.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘biomod2’
  All declared Imports should be used.
File ‘SPODT/libs/SPODT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 8 marked Latin-1 strings
  Note: found 83 marked UTF-8 strings
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs  10.4Mb
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘ggplot2’
  All declared Imports should be used.
installed size is 50.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  48.1Mb
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    libs  26.2Mb
File ‘sROC/libs/sROC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘shinyFiles’
  All declared Imports should be used.
Running ‘testthat.R’ [30s/38s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > #    Copyright 2015 Province of British Columbia
  > #
  > #    Licensed under the Apache License, Version 2.0 (the "License");
  > #    you may not use this file except in compliance with the License.
  > #    You may obtain a copy of the License at
  > #
  > #       http://www.apache.org/licenses/LICENSE-2.0
  > #
  > #    Unless required by applicable law or agreed to in writing, software
  > #    distributed under the License is distributed on an "AS IS" BASIS,
  > #    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  > #    See the License for the specific language governing permissions and
  > #    limitations under the License.
  > 
  > library(testthat)
  > library(ssdtools)
  
  Attaching package: 'ssdtools'
  
  The following objects are masked from 'package:stats':
  
      dgamma, dweibull, pgamma, pweibull, qgamma, qweibull, rgamma,
      rweibull
  
  > 
  > test_check("ssdtools")
  ── 1. Failure: ssd_gof fitdistscens (@test-gof.R#46)  ──────────────────────────
  as.data.frame(ssd_gof(fluazinam_dists)) not equal to structure(...).
  Attributes: < Component "row.names": Modes: numeric, character >
  Attributes: < Component "row.names": target is numeric, current is character >
  
  ── 2. Failure: manual (@test-schwarz-tillmans.R#24)  ───────────────────────────
  as.data.frame(ssd_gof(dists)) not equal to structure(...).
  Attributes: < Component "row.names": Modes: numeric, character >
  Attributes: < Component "row.names": target is numeric, current is character >
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 269 | SKIPPED: 0 | WARNINGS: 12 | FAILED: 2 ]
  1. Failure: ssd_gof fitdistscens (@test-gof.R#46) 
  2. Failure: manual (@test-schwarz-tillmans.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
possible bashism in configure line 19 ('command' with option other than -p):
  if [ $(command -v pkg-config) ]; then
  possible bashism in configure line 33 ($(OS|MACH)TYPE):
  elif [[ "$OSTYPE" == "darwin"* ]]; then
  possible bashism in configure line 33 (alternative test command ([[ foo ]] should be [ foo ])):
  elif [[ "$OSTYPE" == "darwin"* ]]; then
  possible bashism in configure line 33 (should be 'b = a'):
  elif [[ "$OSTYPE" == "darwin"* ]]; then
  possible bashism in configure line 34 ('command' with option other than -p):
    if [ $(command -v brew) ]; then
  possible bashism in configure line 38 (should be '.', not 'source'):
      source autobrew
installed size is 80.1Mb
  sub-directories of 1Mb or more:
    libs  79.7Mb
File ‘sspline/libs/sspline.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stabledist’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘stacomir.Rmd’ using rmarkdown
Quitting from lines 281-303 (stacomir.Rmd) 
Error: processing vignette 'stacomir.Rmd' failed with diagnostics:
abs(round(sum(datasub$value, na.rm = TRUE), 2) - round(sum(datasub2$value,  .... is not TRUE
--- failed re-building ‘stacomir.Rmd’

SUMMARY: processing the following file failed:
  ‘stacomir.Rmd’

Error: Vignette re-building failed.
Execution halted
stkde: no visible global function definition for ‘npudensbw’
stkde: no visible global function definition for ‘npudens’
stkde: no visible global function definition for ‘quantile’
stkde: no visible global function definition for ‘heat.colors’
stkde: no visible global function definition for ‘par’
stkde: no visible global function definition for ‘image’
stkde: no visible global function definition for ‘contour’
stkde.base: no visible global function definition for ‘npudensbw’
stkde.base: no visible global function definition for ‘npudens’
stkde.sig: no visible global function definition for ‘SpatialPoints’
stkde.sig: no visible global function definition for ‘spsample’
stkde.sig: no visible global function definition for ‘bbox’
stkde.sig: no visible global function definition for ‘quantile’
stkde.sig: no visible global function definition for ‘heat.colors’
stkde.sig: no visible global function definition for ‘par’
stkde.sig: no visible global function definition for ‘image’
stkde.sig: no visible global function definition for ‘contour’
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    include  10.3Mb
    lib       3.0Mb
File ‘starma/libs/starma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘STAR/libs/STAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc   1.9Mb
    nc    4.5Mb
Running examples in ‘stars-Ex.R’ failed
The error most likely occurred in:

> ### Name: st_transform
> ### Title: transform features, or warp/resample grids in stars objects to a
> ###   new coordinate reference system
> ### Aliases: st_transform st_transform.stars st_transform_proj.stars
> 
> ### ** Examples
> 
> geomatrix = system.file("tif/geomatrix.tif", package = "stars")
> (x = read_stars(geomatrix))
stars object with 2 dimensions and 1 attribute
attribute(s):
 geomatrix.tif  
 Min.   : 74.0  
 1st Qu.:107.0  
 Median :123.0  
 Mean   :126.8  
 3rd Qu.:132.0  
 Max.   :255.0  
dimension(s):
  from to  offset delta                       refsys point values    
x    1 20 1841002   1.5 PROJCS["WGS 84 / UTM zone...  TRUE   NULL [x]
y    1 20 1144003  -1.5 PROJCS["WGS 84 / UTM zone...  TRUE   NULL [y]
sheared raster with parameters: -5 -5 
> new = st_crs(4326)
> y = st_transform(x, new)
Error in sf_project(from, to, cc) : 
  no arguments in initialization list: PROJCS["WGS 84 / UTM zone 11N",
    GEOGCS["WGS 84",
        DATUM["WGS_1984",
            SPHEROID["WGS 84",6378137,298.257223563,
                AUTHORITY["EPSG","7030"]],
            AUTHORITY["EPSG","6326"]],
        PRIMEM["Greenwich",0,
            AUTHORITY["EPSG","8901"]],
        UNIT["degree",0.0174532925199433,
            AUTHORITY["EPSG","9122"]],
        AUTHORITY["EPSG","4326"]],
    PROJECTION["Transverse_Mercator"],
    PARAMETER["latitude_of_origin",0],
    PARAMETER["central_meridian",-117],
    PARAMETER["scale_factor",0.9996],
    PARAMETER["false_easting",500000],
    PARAMETER["false_northing",0],
    UNIT["metre",1,
        AUTHORITY["EPSG","9001"]],
    AXIS["Easting",EAST],
    AXIS["Northing",NORTH],
    AUTHORITY["EPSG","32611"]]
Calls: st_transform ... st_transform.stars -> transform_curvilinear -> sf_project
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘stars1.Rmd’ using rmarkdown
--- finished re-building ‘stars1.Rmd’

--- re-building ‘stars2.Rmd’ using rmarkdown
--- finished re-building ‘stars2.Rmd’

--- re-building ‘stars3.Rmd’ using rmarkdown
--- finished re-building ‘stars3.Rmd’

--- re-building ‘stars4.Rmd’ using rmarkdown
--- finished re-building ‘stars4.Rmd’

--- re-building ‘stars5.Rmd’ using rmarkdown
Quitting from lines 129-132 (stars5.Rmd) 
Error: processing vignette 'stars5.Rmd' failed with diagnostics:
no arguments in initialization list: PROJCS["NAD83 / North Carolina",
    GEOGCS["NAD83",
        DATUM["North_American_Datum_1983",
            SPHEROID["GRS 1980",6378137,298.257222101,
                AUTHORITY["EPSG","7019"]],
            TOWGS84[0,0,0,0,0,0,0],
            AUTHORITY["EPSG","6269"]],
        PRIMEM["Greenwich",0,
            AUTHORITY["EPSG","8901"]],
        UNIT["degree",0.0174532925199433,
            AUTHORITY["EPSG","9122"]],
        AUTHORITY["EPSG","4269"]],
    PROJECTION["Lambert_Conformal_Conic_2SP"],
    PARAMETER["standard_parallel_1",36.16666666666666],
    PARAMETER["standard_parallel_2",34.33333333333334],
    PARAMETER["latitude_of_origin",33.75],
    PARAMETER["central_meridian",-79],
    PARAMETER["false_easting",609601.22],
    PARAMETER["false_northing",0],
    UNIT["metre",1,
        AUTHORITY["EPSG","9001"]],
    AXIS["X",EAST],
    AXIS["Y",NORTH],
    AUTHORITY["EPSG","32119"]]
--- failed re-building ‘stars5.Rmd’

SUMMARY: processing the following file failed:
  ‘stars5.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   5.1Mb
File ‘staTools/libs/staTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
Running examples in ‘statsr-Ex.R’ failed
The error most likely occurred in:

> ### Name: bandit_posterior
> ### Title: bandit posterior
> ### Aliases: bandit_posterior
> 
> ### ** Examples
> 
> data = data.frame(machine = c(1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L), 
+                   outcome = c("W", "L", "W", "L", "L", "W", "L", "L", "L", "W"))
> bandit_posterior(data)
m1_good m2_good 
    0.5     0.5 
> plot_bandit_posterior(data)
Warning: `data_frame()` is deprecated as of tibble 1.1.0.
Please use `tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Error: Assigned data `prior` must be compatible with row subscript `1`.
✖ 1 row must be assigned.
✖ Assigned data has 2 rows.
ℹ Only vectors of size 1 are recycled.
Backtrace:
    █
 1. └─statsr::plot_bandit_posterior(data)
 2.   ├─base::`[<-`(...)
 3.   └─tibble:::`[<-.tbl_df`(...)
 4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 5.       └─tibble:::vectbl_recycle_rhs(...)
 6.         └─base::tryCatch(...)
 7.           └─base:::tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)
Execution halted
Namespaces in Imports field not imported from:
  ‘gbm’ ‘ggfortify’ ‘tibble’ ‘tidyverse’
  All declared Imports should be used.
File ‘STB/libs/STB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   5.0Mb
File ‘steadyICA/libs/steadyICA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘rlist’ ‘tm’ ‘zoo’
  All declared Imports should be used.
File ‘steepness/libs/steepness.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
File ‘StepwiseTest/libs/StepwiseTest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘stlplus/libs/stlplus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘tm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘huge’ ‘readr’ ‘scales’ ‘shinyjs’
  All declared Imports should be used.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R          2.1Mb
    datasets   2.6Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.7Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Namespace in Imports field not imported from: ‘knitcitations’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘BSgenome’ ‘BiocManager’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘Hmisc’ ‘RColorBrewer’ ‘Rcpp’ ‘readr’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Namespace in Imports field not imported from: ‘bnlearn’
  All declared Imports should be used.
File ‘strat/libs/strat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ks’
  All declared Imports should be used.
Found the following significant warnings:
  BIRCH/CFTree.cpp:18:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/stream.Rcheck/00install.out’ for details.
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  12.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gWidgets2tcltk’
  All declared Imports should be used.
File ‘stsm/libs/stsm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘pls’ ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘UpSetR’ ‘alluvial’ ‘gridBase’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘V8’ ‘bsplus’ ‘colourpicker’ ‘dplyr’ ‘grDevices’ ‘graphics’
  ‘jsonlite’ ‘shinyjs’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lwgeom’
  All declared Imports should be used.
File ‘SummaryLasso/libs/SummaryLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.4Mb
File ‘Sunder/libs/Sunder.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   2.0Mb
.p.1gen: warning in formatC(id, wid = 6): partial argument match of
  'wid' to 'width'
.p.1gen: warning in formatC(s, wid = 4): partial argument match of
  'wid' to 'width'
.p.1gen: warning in formatC(format(c(round(m, digits = digits),
  0.735))[1], wid = 7, dig = 3): partial argument match of 'dig' to
  'digits'
.p.1gen: warning in formatC(format(c(round(m, digits = digits),
  0.735))[1], wid = 7, dig = 3): partial argument match of 'wid' to
  'width'
predict.pelora: warning in matrix(c((1/(1 + exp(-(X[, 1:(noc[i] + 1)]
  %*% koeff))))), nc = 1): partial argument match of 'nc' to 'ncol'
ridge.coef: warning in diag(apply(X, 2, var) * lambda * nrow(X), nr =
  ncol(X)): partial argument match of 'nr' to 'nrow'
aggtrees: no visible global function definition for ‘predict’
coef.pelora: no visible global function definition for ‘fitted’
dlda: no visible binding for global variable ‘var’
logreg: no visible global function definition for ‘glm’
logreg: no visible binding for global variable ‘binomial’
logreg: no visible global function definition for ‘predict’
plot.pelora: no visible global function definition for ‘text’
plot.wilma: no visible global function definition for ‘fitted’
plot.wilma: no visible global function definition for ‘text’
predict.pelora: no visible global function definition for ‘fitted’
predict.pelora: no visible global function definition for ‘coef’
predict.wilma: no visible global function definition for ‘fitted’
print.wilma: no visible global function definition for ‘fitted’
ridge.coef: no visible binding for global variable ‘var’
sign.change: no visible binding for global variable ‘cov’
standardize.genes: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  binomial coef cov fitted glm predict sd text var
Consider adding
  importFrom("graphics", "text")
  importFrom("stats", "binomial", "coef", "cov", "fitted", "glm",
             "predict", "sd", "var")
to your NAMESPACE file.
File ‘supclust/libs/supclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Namespaces in Imports field not imported from:
  ‘R.matlab’ ‘fBasics’ ‘spls’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘mvtnorm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘learnr’
  All declared Imports should be used.
File ‘survAUC/libs/survAUC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘survC1/libs/survC1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.2Mb
    libs   2.0Mb
File ‘surveybootstrap/libs/surveybootstrap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 157.4Mb
  sub-directories of 1Mb or more:
    libs  155.9Mb
File ‘survIDINRI/libs/survIDINRI.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.2Mb
    doc    3.3Mb
File ‘survivalROC/libs/survivalROC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
File ‘survSNP/libs/survSNP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   7.2Mb
File ‘svcm/libs/svcm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SVMMatch/libs/SVMMatch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘svmpath/libs/svmpath.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi30spec.o’, ‘mi35mps.o’,
      ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘_gfortran_st_rewind’, possibly from ‘rewind’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi10unix.o’, ‘mi35mps.o’, ‘mi40bfil.o’
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’
File ‘svmpath/libs/svmpath.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lazyeval’ ‘lubridate’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘scales’ ‘utils’
  All declared Imports should be used.
Running examples in ‘SWMPrExtension-Ex.R’ failed
The error most likely occurred in:

> ### Name: seasonal_dot
> ### Title: Seasonal Dot Plot
> ### Aliases: seasonal_dot seasonal_dot.swmpr
> 
> ### ** Examples
> 
> dat_wq <- elksmwq
> #dat_wq <- subset(dat_wq, subset = c('2010-01-01 0:00', '2017-01-01 0:00'))
> dat_wq <- qaqc(dat_wq, qaqc_keep = c(0, 3, 5))
> 
> x <-
+   seasonal_dot(dat_wq, param = 'do_mgl'
+                , lm_trend = TRUE
+                , lm_lab = TRUE
+                , plot_title = TRUE)
Error: Aesthetics must be either length 1 or the same as the data (48): y
Backtrace:
    █
 1. ├─SWMPrExtension::seasonal_dot(...)
 2. └─SWMPrExtension:::seasonal_dot.swmpr(...)
 3.   ├─ggplot2::ggplot_build(plt)
 4.   └─ggplot2:::ggplot_build.ggplot(plt)
 5.     └─ggplot2:::by_layer(function(l, d) l$compute_aesthetics(d, plot))
 6.       └─ggplot2:::f(l = layers[[i]], d = data[[i]])
 7.         └─l$compute_aesthetics(d, plot)
 8.           └─ggplot2:::f(..., self = self)
 9.             └─ggplot2:::check_aesthetics(evaled, n)
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
File ‘SynchWave/libs/SynchWave.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    extdata   3.4Mb
Namespace in Imports field not imported from: ‘metR’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Namespaces in Imports field not imported from:
  ‘gee’ ‘survival’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gibble’ ‘rlang’
  All declared Imports should be used.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    java  11.5Mb
File ‘tagcloud/libs/tagcloud.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘devEMF’ ‘segmented’ ‘smoother’ ‘tools’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   5.6Mb
Namespace in Imports field not imported from: ‘jiebaR’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘dplyr’ ‘igraph’ ‘tm’ ‘wordcloud2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘drat’ ‘plyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘lazyeval’ ‘rlang’ ‘tidyr’
  All declared Imports should be used.
Running ‘testthat.R’ [31s/51s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(taxa)
  
  Attaching package: 'taxa'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  > 
  > test_check("taxa")
  ── 1. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers
  test_obj$data$my_data$taxon_id not equal to c("j", "i").
  names for target but not for current
  
  ── 2. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers
  test_obj$data$my_data$taxon_id not equal to c("j", "i").
  names for target but not for current
  
  ── 3. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers
  test_obj$data$my_data$taxon_id not equal to c("j", "i").
  names for target but not for current
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 607 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers.R#52) 
  2. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers.R#56) 
  3. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers.R#60) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘tbart/libs/tbart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘PerformanceAnalytics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘glmnet’ ‘quadprog’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    tklibs   4.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.9Mb
    libs   1.2Mb
installed size is 33.8Mb
  sub-directories of 1Mb or more:
    libs  32.5Mb
File ‘TDboost/libs/TDboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.

Requires orphaned package: ‘d3heatmap’
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    apps   2.8Mb
    libs   8.6Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘tidyr’
  All declared Imports should be used.
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  17.2Mb
File ‘tensorA/libs/tensorA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 32.0Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs  29.4Mb
possible bashism in configure line 34 ($(OS|MACH)TYPE):
    case "$OSTYPE" in "darwin"*)
  possible bashism in configure line 42 (should be '.', not 'source'):
      source autobrew
File ‘TESS/libs/TESS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘par-7269706c6579’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   2.1Mb
Namespaces in Imports field not imported from:
  ‘stringi’ ‘utils’
  All declared Imports should be used.
File ‘testforDEP/libs/testforDEP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    2.9Mb
    libs   5.2Mb
Note: found 10051 marked UTF-8 strings
  Note: found 10523 strings marked as "bytes"
Namespace in Imports field not imported from: ‘lexicon’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘parallel’ ‘tidyr’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
File ‘textreuse/libs/textreuse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
File ‘tgp/libs/tgp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    rda    7.1Mb
Namespace in Imports field not imported from: ‘proxy’
  All declared Imports should be used.
installed size is 31.5Mb
  sub-directories of 1Mb or more:
    libs  31.2Mb
Namespace in Imports field not imported from: ‘broomExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mix’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Evomorph’ ‘cowplot’ ‘factoextra’ ‘gridExtra’ ‘lme4’ ‘lsr’ ‘plotly’
  ‘png’ ‘shapes’
  All declared Imports should be used.
Running examples in ‘tidymv-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot_difference
> ### Title: Plot difference smooth from a GAM.
> ### Aliases: plot_difference
> 
> ### ** Examples
> 
> library(mgcv)
Loading required package: nlme
This is mgcv 1.8-31. For overview type 'help("mgcv-package")'.
> set.seed(10)
> data <- gamSim(4)
Factor `by' variable example
> model <- gam(y ~ fac + s(x2) + s(x2, by = fac) + s(x0), data = data)
> 
> plot_difference(model, x2, list(fac = c("1", "2")))
Error in table(predictors$Terms) - table(predictors[predictors$Label %in%  : 
  non-conformable arrays
Calls: plot_difference -> %>% -> eval -> eval
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘plot-smooths.Rmd’ using rmarkdown
Quitting from lines 172-177 (plot-smooths.Rmd) 
Error: processing vignette 'plot-smooths.Rmd' failed with diagnostics:
non-conformable arrays
--- failed re-building ‘plot-smooths.Rmd’

--- re-building ‘predict-gam.Rmd’ using rmarkdown
--- finished re-building ‘predict-gam.Rmd’

SUMMARY: processing the following file failed:
  ‘plot-smooths.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Running ‘testthat.R’ [21s/49s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidytext)
  > 
  > test_check("tidytext")
  ── 1. Failure: Can tidy corpus from tm package (@test-corpus-tidiers.R#15)  ────
  paste(as.character(ovid[[1]]), collapse = " ") not equal to td$text[1].
  names for current but not for target
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 297 | SKIPPED: 1 | WARNINGS: 2 | FAILED: 1 ]
  1. Failure: Can tidy corpus from tm package (@test-corpus-tidiers.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘curl’ ‘keyring’ ‘nlme’ ‘rgdal’ ‘stringi’ ‘usethis’
  All declared Imports should be used.
Found the following significant warnings:
  ref.cpp:24:14: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
  ref.cpp:35:14: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
  ref.cpp:50:16: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
  ref.cpp:61:16: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/tidyxl.Rcheck/00install.out’ for details.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
File ‘tidyxl/libs/tidyxl.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
    Object: ‘xlex.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tiff/libs/tiff.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘timma/libs/timma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘broom’ ‘tibble’
  All declared Imports should be used.
File ‘TKF/libs/TKF.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tkrplot/libs/tkrplot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    examples  15.0Mb
    include    3.0Mb
installed size is 25.4Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
File ‘tmg/libs/tmg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tmvnsim/libs/tmvnsim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tmvtnorm/libs/tmvtnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/tolBasis.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’ ‘jsonlite’
  All declared Imports should be used.
File ‘TopKLists/libs/TopKLists.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘jmvcore’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Note: found 64 marked Latin-1 strings
  Note: found 548 marked UTF-8 strings
File ‘tpr/libs/tpr.so’:
  Found ‘_ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’
File ‘tpr/libs/tpr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 153 marked Latin-1 strings
  Note: found 108 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘V8’ ‘colorspace’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.7Mb
Namespace in Imports field not imported from: ‘neuralnet’
  All declared Imports should be used.
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
File ‘trapezoid/libs/trapezoid.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    extdata   1.4Mb
    libs     12.5Mb
File ‘treeperm/libs/treeperm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is 126.9Mb
  sub-directories of 1Mb or more:
    doc     3.8Mb
    libs  122.1Mb
File ‘TrialSize/libs/TrialSize.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
File ‘triebeard/libs/triebeard.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  rfmod.c:467:1: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/trimTrees.Rcheck/00install.out’ for details.
File ‘trimTrees/libs/trimTrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
Namespaces in Imports field not imported from:
  ‘here’ ‘htmltools’ ‘scales’ ‘stringr’
  All declared Imports should be used.
File ‘truncgof/libs/truncgof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
File ‘tsc/libs/tsc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   7.7Mb
File ‘tseriesChaos/libs/tseriesChaos.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘tsibble’
  All declared Imports should be used.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.8Mb
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
.help.ESS: no visible global function definition for ‘index.search’
TransSphere : ttin: no visible global function definition for ‘t.test’
TransSphere: no visible global function definition for ‘sd’
TransSphere: no visible global function definition for ‘quantile’
TransSphere: no visible global function definition for ‘pt’
Undefined global functions or variables:
  index.search pt quantile sd t.test
Consider adding
  importFrom("stats", "pt", "quantile", "sd", "t.test")
to your NAMESPACE file.
File ‘tspmeta/libs/tspmeta.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘forecastHybrid’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘shinyAce’ ‘shinyjs’
  All declared Imports should be used.
File ‘tvd/libs/tvd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘TwoCop/libs/TwoCop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘TwoPhaseInd/libs/TwoPhaseInd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc     6.4Mb
    ubinc   2.0Mb
File ‘ucminf/libs/ucminf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘plotly’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  ‘shinythemes’ ‘zip’
  All declared Imports should be used.
installed size is 33.4Mb
  sub-directories of 1Mb or more:
    doc         6.9Mb
    dummydata   1.4Mb
    libs       23.7Mb
File ‘udunits2/libs/udunits2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data      2.0Mb
    extdata   2.3Mb
    libs      3.0Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
Namespaces in Imports field not imported from:
  ‘extraDistr’ ‘logitnorm’ ‘nakagami’ ‘tibble’
  All declared Imports should be used.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.6Mb
    libs   9.9Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
File ‘urca/libs/urca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    data  26.4Mb
Imports includes 32 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Running examples in ‘ushr-Ex.R’ failed
The error most likely occurred in:

> ### Name: summarize_model
> ### Title: Summarize model output
> ### Aliases: summarize_model
> 
> ### ** Examples
> 
> 
> set.seed(1234567)
> 
> simulated_data <- simulate_data(nsubjects = 20)
Joining, by = "id"
> 
> model_output <- ushr(data = simulated_data)
Warning in sqrt(diag(fisher_info)) : NaNs produced
Warning in sqrt(diag(fisher_info)) : NaNs produced
Warning in sqrt(diag(fisher_info)) : NaNs produced
Warning in sqrt(diag(fisher_info)) : NaNs produced
> 
> summarize_model(model_output, data = simulated_data)
Joining, by = c("id", "Model")
Joining, by = "id"
Error: Assigned data `values` must be compatible with existing data.
ℹ Error occurred for column `ShortLifespan`.
✖ No common type for `value` <character> and `x` <double>.
Backtrace:
     █
  1. └─ushr::summarize_model(model_output, data = simulated_data)
  2.   └─`%>%`(...)
  3.     ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  4.     └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  5.       └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  6.         └─ushr:::`_fseq`(`_lhs`)
  7.           └─magrittr::freduce(value, `_function_list`)
  8.             ├─base::withVisible(function_list[[k]](value))
  9.             └─function_list[[k]](value)
 10.               └─base::replace(., is.na(.), "")
 11.                 ├─base::`[<-`(`*tmp*`, list, value = "")
 12.                 └─tibble:::`[<-.tbl_df`(`*tmp*`, list, value = "")
 13.                   └─tibble:::tbl_subassign_matrix(x, j, value, j_arg, substitute(va
Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   6.4Mb
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘stringdist’ ‘utils’
  All declared Imports should be used.
File ‘uuid/libs/uuid.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
File ‘valorate/libs/valorate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Namespaces in Imports field not imported from:
  ‘rstudioapi’ ‘testthat’
  All declared Imports should be used.
File ‘varband/libs/varband.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘matrixcalc’ ‘saemix’
  All declared Imports should be used.
File ‘vbdm/libs/vbdm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘vbsr/libs/vbsr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
File ‘Vdgraph/libs/Vdgraph.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘vdg/libs/vdg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘freetypeharfbuzz’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    doc    1.2Mb
    help   2.9Mb
Namespaces in Imports field not imported from:
  ‘sp’ ‘viridis’
  All declared Imports should be used.
File ‘VIFCP/libs/VIFCP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘VIGoR/libs/VIGoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 50.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  49.3Mb
File ‘vines/libs/vines.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘DT’ ‘plyr’ ‘reshape’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘diptest’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    libs  26.5Mb
Namespace in Imports field not imported from: ‘sqldf’
  All declared Imports should be used.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc           4.3Mb
    docjs         1.4Mb
    htmlwidgets   4.0Mb
File ‘vita/libs/vita.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ingredients’
  All declared Imports should be used.
installed size is 46.7Mb
  sub-directories of 1Mb or more:
    libs  46.3Mb
Namespaces in Imports field not imported from:
  ‘iterators’ ‘knitr’ ‘purrr’ ‘testthat’
  All declared Imports should be used.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
Namespace in Imports field not imported from: ‘haven’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘XML’ ‘checkmate’ ‘gstat’ ‘intervals’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘EnvStats’ ‘shiny’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tibble’
  All declared Imports should be used.
File ‘waffect/libs/waffect.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘waffect.o’
File ‘waffect/libs/waffect.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 63.2Mb
  sub-directories of 1Mb or more:
    libs  61.9Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ENMeval’ ‘RColorBrewer’ ‘XML’ ‘dismo’ ‘dplyr’ ‘leaflet.extras’
  ‘maptools’ ‘raster’ ‘rgdal’ ‘rgeos’ ‘rmarkdown’ ‘shinyjs’
  ‘shinythemes’ ‘spThin’ ‘spocc’ ‘testthat’ ‘zip’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   6.4Mb
File ‘wavelets/libs/wavelets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
File ‘wavethresh/libs/wavethresh.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘zoo’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    client   9.6Mb
    doc      1.0Mb
File ‘webreadr/libs/webreadr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘shiny’ ‘tidyselect’
  All declared Imports should be used.
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘later’
  All declared Imports should be used.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    doc   11.9Mb
    libs   1.5Mb
File ‘weightedScores/libs/weightedScores.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
Namespaces in Imports field not imported from:
  ‘drc’ ‘imputeTestbench’
  All declared Imports should be used.
File ‘wingui/libs/wingui.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    bn   7.1Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘DescTools’ ‘HydeNet’ ‘RBGL’ ‘Rgraphviz’ ‘arules’ ‘bnlearn’
  ‘dplyr’ ‘graph’ ‘igraph’ ‘linkcomm’ ‘missRanger’ ‘parallel’ ‘psych’
  ‘rhandsontable’ ‘rintrojs’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’
  ‘shinycssloaders’ ‘shinydashboard’ ‘tools’ ‘visNetwork’
  All declared Imports should be used.
File ‘WMCapacity/libs/WMCapacity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
possible bashism in configure line 49 (test -a/-o):
  if test ${java_version_maj} -ge 5 || \
      test ${java_version_maj} -eq 1 -a ${java_version_min} -ge 5;
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.7Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
Package suggested but not available for checking: ‘ROTS’
Packages unavailable to check Rd xrefs: ‘cleaver’, ‘ROTS’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   7.2Mb
Namespace in Imports field not imported from: ‘simts’
  All declared Imports should be used.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-clang/x13binary.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    bin   5.4Mb
installed size is 36.5Mb
  sub-directories of 1Mb or more:
    libs  35.6Mb
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    java  26.2Mb
File ‘XMRF/libs/XMRF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘XNomial/libs/XNomial.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ggdendro’
  All declared Imports should be used.
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
Found the following significant warnings:
  Warning: replacing previous import ‘lubridate::intersect’ by ‘raster::intersect’ when loading ‘xROI’
  Warning: replacing previous import ‘lubridate::union’ by ‘raster::union’ when loading ‘xROI’
See ‘/data/gannet/ripley/R/packages/tests-clang/xROI.Rcheck/00install.out’ for details.
File ‘xseq/libs/xseq.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    include   3.5Mb
    libs      1.9Mb
File ‘yakmoR/libs/yakmoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘miniUI’ ‘shinyBS’
  All declared Imports should be used.
installed size is 41.5Mb
  sub-directories of 1Mb or more:
    libs  41.2Mb
Namespace in Imports field not imported from: ‘ghyp’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   3.6Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘testthat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘moonBook’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
asp: no visible global function definition for ‘as.formula’
asp: no visible global function definition for ‘var’
aspm: no visible binding for global variable ‘X.Declan’
aspm: no visible binding for global variable ‘Z.Jaida’
aspm: no visible binding for global variable ‘group.vec.Handan’
aspm: no visible global function definition for ‘as.formula’
aspm: no visible global function definition for ‘glm’
aspm: no visible global function definition for ‘binomial’
aspm: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.
Running ‘testthat.R’ [11s/56s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(apa)
  > 
  > test_check("apa")
  ── 1. Error: Output for anova_apa: repeated-measures ANOVA (@test-anova-apa.R#13
  Assigned data `<list>` must be compatible with existing data.
  ℹ Error occurred for column `df_n`.
  ✖ No common type for `value` <character> and `x` <double>.
  Backtrace:
    1. apa::anova_apa(...)
    2. apa:::anova_apa_afex(x, effect, sph_corr, es, format, info, print)
    7. tibble:::`[<-.tbl_df`(...)
    8. tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    9. tibble:::tbl_subassign_row(xj, i, value, value_arg)
   10. base::tryCatch(...)
   11. base:::tryCatchList(expr, classes, parentenv, handlers)
   12. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   13. value[[3L]](cond)
  
  ── 2. Error: Output for anova_apa: factorial repeated-measures ANOVA (@test-anov
  Assigned data `<list>` must be compatible with existing data.
  ℹ Error occurred for column `df_n`.
  ✖ No common type for `value` <character> and `x` <double>.
  Backtrace:
    1. apa::anova_apa(...)
    2. apa:::anova_apa_afex(x, effect, sph_corr, es, format, info, print)
    7. tibble:::`[<-.tbl_df`(...)
    8. tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    9. tibble:::tbl_subassign_row(xj, i, value, value_arg)
   10. base::tryCatch(...)
   11. base:::tryCatchList(expr, classes, parentenv, handlers)
   12. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   13. value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 105 | SKIPPED: 0 | WARNINGS: 9 | FAILED: 2 ]
  1. Error: Output for anova_apa: repeated-measures ANOVA (@test-anova-apa.R#135) 
  2. Error: Output for anova_apa: factorial repeated-measures ANOVA (@test-anova-apa.R#181) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘bayesCT.Rmd’ using rmarkdown
--- finished re-building ‘bayesCT.Rmd’

--- re-building ‘binomial.Rmd’ using rmarkdown

Attaching package: 'bayesCT'

The following object is masked from 'package:stats':

    simulate

--- finished re-building ‘binomial.Rmd’

--- re-building ‘normal.Rmd’ using rmarkdown

Attaching package: 'bayesCT'

The following object is masked from 'package:stats':

    simulate

--- finished re-building ‘normal.Rmd’

sh: line 1: 38545 CPU time limit exceeded (core dumped) '/data/gannet/ripley/R/R-devel/bin/R' --vanilla --no-echo > '/tmp/RtmpWLqQI4/working_dir/RtmpQlzJuO/file836f501fed7' 2>&1 < '/tmp/RtmpWLqQI4/working_dir/RtmpQlzJuO/file836f43534b08'
Warning: elapsed-time limit of 30 minutes reached for sub-process
--- re-building ‘time-to-event.Rmd’ using rmarkdown

Attaching package: 'bayesCT'

The following object is masked from 'package:stats':

    simulate

SUMMARY: processing the following file failed:
  ‘time-to-event.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'bcmapsdata', 'lwgeom'
Packages required but not available: 'tmaptools', 'tmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
bigglm.RODBC: no visible global function definition for ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘sqlGetResults’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbSendQuery’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbSendQuery’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘fetch’
Undefined global functions or variables:
  dbClearResult dbSendQuery fetch odbcQuery sqlGetResults
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/Biograph.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [7s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(biscale)
  > 
  > test_check("biscale")
  ── 1. Error: sf warning is triggered (@test_bi_class.R#10)  ────────────────────
  All columns in a tibble must be vectors.
  ✖ Column `geometry` is a `sfc_POLYGON/sfc` object.
  Backtrace:
    1. testthat::expect_warning(...)
    6. biscale::bi_class(...)
    8. dplyr:::mutate.data.frame(...)
   11. dplyr::tbl_df(.data)
   13. tibble:::as_tibble.data.frame(data, .name_repair = "check_unique")
   14. tibble:::lst_to_tibble(unclass(x), .rows, .name_repair)
   15. tibble:::check_valid_cols(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 82 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: sf warning is triggered (@test_bi_class.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘broom_mixed_intro.rmd’ using rmarkdown

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

Registered S3 methods overwritten by 'broom.mixed':
  method         from 
  augment.lme    broom
  augment.merMod broom
  glance.lme     broom
  glance.merMod  broom
  glance.stanreg broom
  tidy.brmsfit   broom
  tidy.gamlss    broom
  tidy.lme       broom
  tidy.merMod    broom
  tidy.rjags     broom
  tidy.stanfit   broom
  tidy.stanreg   broom
Loading required package: brms
Loading required package: Rcpp
Loading 'brms' package (version 2.12.0). Useful instructions
can be found by typing help('brms'). A more detailed introduction
to the package is available through vignette('brms_overview').

Attaching package: 'brms'

The following object is masked from 'package:stats':

    ar

Loading required package: dotwhisker
Loading required package: ggplot2
Warning: `data_frame()` is deprecated as of tibble 1.1.0.
Please use `tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Quitting from lines 68-82 (broom_mixed_intro.rmd) 
Error: processing vignette 'broom_mixed_intro.rmd' failed with diagnostics:
Aesthetics must be either length 1 or the same as the data (6): xmin and xmax
--- failed re-building ‘broom_mixed_intro.rmd’

SUMMARY: processing the following file failed:
  ‘broom_mixed_intro.rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘lwgeom’
Running examples in ‘c14bazAAR-Ex.R’ failed
The error most likely occurred in:

> ### Name: determine_country_by_coordinate
> ### Title: Functions to improve the country attribution in a
> ###   *c14_date_list*
> ### Aliases: determine_country_by_coordinate
> ###   determine_country_by_coordinate.default
> ###   determine_country_by_coordinate.c14_date_list country_attribution
> ###   finalize_country_name finalize_country_name.default
> ###   finalize_country_name.c14_date_list standardize_country_name
> ###   standardize_country_name.default
> ###   standardize_country_name.c14_date_list
> 
> ### ** Examples
> 
> library(magrittr)
> example_c14_date_list %>%
+   determine_country_by_coordinate() %>%
+   standardize_country_name() %>%
+   finalize_country_name()
Error: R packages sf, rworldxtra, rgeos, lwgeom needed for this function to work. Please install with install.packages(c('sf', 'rworldxtra', 'rgeos', 'lwgeom'))
Execution halted
Package unavailable to check Rd xrefs: ‘SpatialPosition’
Running examples in ‘cartography-Ex.R’ failed
The error most likely occurred in:

> ### Name: smoothLayer
> ### Title: Smooth Layer
> ### Aliases: smoothLayer
> 
> ### ** Examples
> 
> library(sf)
Linking to GEOS 3.7.1, GDAL 2.3.2, PROJ 5.2.0
> mtq <- st_read(system.file("gpkg/mtq.gpkg", package="cartography"))
Reading layer `mtq' from data source `/data/gannet/ripley/R/packages/tests-devel/cartography.Rcheck/cartography/gpkg/mtq.gpkg' using driver `GPKG'
Simple feature collection with 34 features and 7 fields
geometry type:  MULTIPOLYGON
dimension:      XY
bbox:           xmin: 690574 ymin: 1592536 xmax: 735940.2 ymax: 1645660
CRS:            32620
> smoothLayer(x = mtq, var = 'POP',
+             span = 4000, beta = 2,
+             mask = mtq, border = NA,
+             col = carto.pal(pal1 = 'wine.pal', n1 = 8),
+             legend.title.txt = "Population\nPotential",
+             legend.pos = "topright", legend.values.rnd = 0)
Error: 'SpatialPosition' package needed for this function to work. Please install it.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘cartography.Rmd’ using rmarkdown
Linking to GEOS 3.7.1, GDAL 2.3.2, PROJ 5.2.0
Quitting from lines 389-424 (cartography.Rmd) 
Error: processing vignette 'cartography.Rmd' failed with diagnostics:
'SpatialPosition' package needed for this function to work. Please install it.
--- failed re-building ‘cartography.Rmd’

--- re-building ‘cheatsheet.Rmd’ using rmarkdown
--- finished re-building ‘cheatsheet.Rmd’

SUMMARY: processing the following file failed:
  ‘cartography.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [4m/18m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(clubSandwich)
  Registered S3 method overwritten by 'clubSandwich':
    method    from    
    bread.mlm sandwich
  > 
  > test_check("clubSandwich")
  ── 1. Failure: Order doesn't matter. (@test_lmerMod.R#153)  ────────────────────
  `Wald_fit` not equal to `Wald_scramble`.
  Component 19: Component 4: Mean relative difference: 1.550445e-08
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 754 | SKIPPED: 11 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Order doesn't matter. (@test_lmerMod.R#153) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘tidyverse’
  All declared Imports should be used.
Running ‘testthat.R’ [13s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(corpus)
  > 
  > test_check("corpus")
  -- 1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161
  invalid 'type' (list) of argument
  Backtrace:
    1. base::strsplit(capture_output(print(loc), width = 76), "\n")
    9. corpus:::print.corpus_text_locate(loc)
   10. corpus:::format.corpus_text_locate(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 612 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘tmap’
Error(s) in re-building vignettes:
--- re-building ‘quick_start_guide.Rmd’ using rmarkdown
trying URL 'http://census.cso.ie/censusasp/saps/boundaries/Census2011_NUTS3_generalised20m.zip'
Content type 'application/x-zip-compressed' length 841102 bytes (821 KB)
==================================================
downloaded 821 KB

Quitting from lines 63-74 (quick_start_guide.Rmd) 
Error: processing vignette 'quick_start_guide.Rmd' failed with diagnostics:
there is no package called 'tmap'
--- failed re-building ‘quick_start_guide.Rmd’

SUMMARY: processing the following file failed:
  ‘quick_start_guide.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘stars’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  WARNING: ignoring environment value of R_HOME
See ‘/data/gannet/ripley/R/packages/tests-devel/datasailr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: possible error in 'glmer(y ~ items + (1 | ': unused argument (REML = FALSE) 
See ‘/data/gannet/ripley/R/packages/tests-devel/difR.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 required but not available: 'lwgeom', 'tmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘test-all.R’ [20s/50s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(eeptools)
  Loading required package: ggplot2
  > 
  > test_check("eeptools")
  ── 1. Failure: moves_calc gets the correct results (@test-calculators.R#210)  ──
  `moves` not equal to `correct_result`.
  Component "sid": Modes: character, numeric
  Component "sid": Attributes: < target is NULL, current is list >
  Component "sid": target is character, current is factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 509 | SKIPPED: 0 | WARNINGS: 29 | FAILED: 1 ]
  1. Failure: moves_calc gets the correct results (@test-calculators.R#210) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(epikit)
  > 
  > test_check("epikit")
  ── 1. Failure: case_fatality_rate_df will add a total row to stratified analysis
  `iris_res` not equal to `iris_n`.
  Incompatible type for column `Species`: x character, y factor
  
  ── 2. Failure: case_fatality_rate_df will add a total row to stratified analysis
  `iris_res` not equal to `iris_n`.
  Incompatible type for column `Species`: x character, y factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 107 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: case_fatality_rate_df will add a total row to stratified analysis (@test-proportion.R#152) 
  2. Failure: case_fatality_rate_df will add a total row to stratified analysis and merge CI (@test-proportion.R#173) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [15s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(estatapi)
  このサービスは、政府統計総合窓口(e-Stat)のAPI機能を使用していますが、サービスの内容は国によって保証されたものではありません。
  > 
  > test_check("estatapi")
  ── 1. Failure: estat_getStatsData processes the API response as expected  ──────
  estat_getStatsData(...) not identical to readRDS("result_getStatsData.rds").
  Objects equal but not identical
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 22 | SKIPPED: 12 | WARNINGS: 7 | FAILED: 1 ]
  1. Failure: estat_getStatsData processes the API response as expected 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(etl)
  Loading required package: 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
  
  > 
  > test_check("etl")
  ── 1. Failure: create ETL works (@test-etl.R#114)  ─────────────────────────────
  `create_etl_package\(path, open = FALSE\)` does not match "active project".
  Actual value: "Package: scorecard\\nTitle: What the Package Does \(One Line, Title Case\)\\nVersion: 0\.0\.0\.9000\\nAuthors@R \(parsed\):\\n    \* First Last <first\.last@example\.com> \[aut, cre\] \(YOUR-ORCID-ID\)\\nDescription: What the package does \(one paragraph\)\.\\nLicense: `use_mit_license\(\)`, `use_gpl3_license\(\)` or friends to pick a\\n    license\\nEncoding: UTF-8\\nLazyData: true\\nRoxygen: list\(markdown = TRUE\)\\nRoxygenNote: 7\.1\.0"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 35 | SKIPPED: 2 | WARNINGS: 2 | FAILED: 1 ]
  1. Failure: create ETL works (@test-etl.R#114) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [31s/34s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fable)
  Loading required package: fabletools
  > 
  > test_check("fable")
  ── 1. Failure: Automatic ETS selection (@test-ets.R#14)  ───────────────────────
  tidy(model(UKLungDeaths[1:24, ], ETS(mdeaths)))$estimate not equal to c(1, 2134).
  names for target but not for current
  
  ── 2. Failure: Manual ETS selection (@test-ets.R#51)  ──────────────────────────
  tidy(refit(fable_fit, USAccDeaths_tbl))$estimate == tidy(fable_fit)$estimate not identical to c(rep(TRUE, 2), rep(FALSE, 12)).
  names for target but not for current
  
  ── 3. Failure: Manual ETS selection (@test-ets.R#62)  ──────────────────────────
  tidy(fable_fit)$estimate[3:14] not identical to c(cmp$level[12], cmp$season[12:2]).
  names for target but not for current
  
  ── 4. Failure: Manual ETS selection (@test-ets.R#87)  ──────────────────────────
  coef$estimate[1:4] not identical to c(0.5, 0.006, 1e-04, 0.975).
  names for target but not for current
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 100 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: Automatic ETS selection (@test-ets.R#14) 
  2. Failure: Manual ETS selection (@test-ets.R#51) 
  3. Failure: Manual ETS selection (@test-ets.R#62) 
  4. Failure: Manual ETS selection (@test-ets.R#87) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘stars’
Running ‘testthat.R’ [43s/133s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggspatial)
  Loading required package: ggplot2
  > 
  > test_check("ggspatial")
  ── 1. Error: stars objects are converted properly by df_spatial (@test-df_spatia
  there is no package called 'stars'
  Backtrace:
   1. stars::read_stars
   2. base::getExportedValue(pkg, name)
   3. base::asNamespace(ns)
   4. base::getNamespace(ns)
   5. base::loadNamespace(name)
   6. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   7. base:::withOneRestart(expr, restarts[[1L]])
   8. base:::doWithOneRestart(return(expr), restart)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 121 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: stars objects are converted properly by df_spatial (@test-df_spatial.R#123) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘lwgeom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘gtfsrouter-Ex.R’ failed
The error most likely occurred in:

> ### Name: gtfs_isochrone
> ### Title: gtfs_isochrone
> ### Aliases: gtfs_isochrone
> 
> ### ** Examples
> 
> berlin_gtfs_to_zip ()
> f <- file.path (tempdir (), "vbb.zip")
> g <- extract_gtfs (f)
> g <- gtfs_timetable (g)
Day not specified; extracting timetable for Saturday
> from <- "Alexanderplatz"
> start_time <- 12 * 3600 + 600
> end_time <- start_time + 600
> ic <- gtfs_isochrone (g,
+                       from = from,
+                       start_time = start_time,
+                       end_time = end_time)
Loading required namespace: geodist
Loading required namespace: lwgeom
Failed with error:  ‘there is no package called ‘lwgeom’’
Error in st_area.sfc(geometry) : 
  package lwgeom required, please install it first
Calls: gtfs_isochrone ... isohull -> <Anonymous> -> <Anonymous> -> st_area.sfc
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘gtfsrouter.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'lwgeom''
Quitting from lines 308-315 (gtfsrouter.Rmd) 
Error: processing vignette 'gtfsrouter.Rmd' failed with diagnostics:
package lwgeom required, please install it first
--- failed re-building ‘gtfsrouter.Rmd’

SUMMARY: processing the following file failed:
  ‘gtfsrouter.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Note: possible error in 'lmer(phen1 ~ x.snp + ': unused argument (family = "binomial") 
See ‘/data/gannet/ripley/R/packages/tests-devel/GWAF.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’.
normalweight: no visible binding for global variable ‘NW_above’
normalweight: no visible binding for global variable ‘NW_below’
obese: no visible global function definition for ‘data’
obese: no visible binding for global variable ‘OB_above’
obese: no visible binding for global variable ‘OB_below’
overweight: no visible global function definition for ‘data’
overweight: no visible binding for global variable ‘OW_above’
overweight: no visible binding for global variable ‘OW_below’
Undefined global functions or variables:
  NW_above NW_below OB_above OB_below OW_above OW_below data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
PlotOptPower: no visible global function definition for ‘bmp’
PlotOptPower: no visible global function definition for
  ‘filled.contour’
PlotOptPower: no visible global function definition for ‘title’
PlotOptPower: no visible global function definition for ‘grey.colors’
PlotOptPower: no visible global function definition for ‘axis’
PlotOptPower: no visible global function definition for ‘polygon’
PlotOptPower: no visible global function definition for ‘legend’
PlotOptPower: no visible global function definition for ‘mtext’
PlotOptPower: no visible global function definition for ‘dev.off’
PlotOptPower: no visible global function definition for
  ‘terrain.colors’
ShowOptDesign: no visible global function definition for ‘head’
diffVariantError: no visible global function definition for ‘pbinom’
predictPoolNCP: no visible global function definition for ‘data’
probDetEqual3: no visible global function definition for ‘dbinom’
probDetEqual3: no visible global function definition for ‘pbinom’
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
Interpol: no visible global function definition for ‘splinefun’
Undefined global functions or variables:
  splinefun
Consider adding
  importFrom("stats", "splinefun")
to your NAMESPACE file.
Package unavailable to check Rd xrefs: ‘lwgeom’
Running examples in ‘isoband-Ex.R’ failed
The error most likely occurred in:

> ### Name: iso_to_sfg
> ### Title: Convert isolines or isobands to sfg object
> ### Aliases: iso_to_sfg
> 
> ### ** Examples
> 
> library(sf)
Linking to GEOS 3.7.1, GDAL 2.3.2, PROJ 5.2.0
> library(ggplot2)
> 
> # Example 1: simple 5x5 matrix
> m <- matrix(c(0, 2, 2, 2, 0,
+               0, 1, 0, 1, 0,
+               0, 1, 0, 0, 0,
+               0, 1, 0, 1, 0,
+               0, 0, 0, 0, 0), 5, 5, byrow = TRUE)
> 
> z <- isolines(1:ncol(m), nrow(m):1, m, c(0.5, 1.5))
> lines <- iso_to_sfg(z)
> x <- st_sf(level = names(lines), geometry = st_sfc(lines))
> ggplot(x) + geom_sf(aes(color = level))
> 
> # Example 2: volcano dataset
> m <- volcano
> b <- isobands((1:ncol(m))/(ncol(m)+1), (nrow(m):1)/(nrow(m)+1), m,
+               10*9:19, 10*10:20)
> bands <- iso_to_sfg(b)
> x <- st_sf(level = as.numeric(sub(":.*", "", names(bands))), geometry = st_sfc(bands))
> ggplot(x) + geom_sf(aes(color = level, fill = level))
> 
> # Example 3: invalid simple features
> m <- matrix(c(1.5, 1.5, 1.5, 1.5, 0.6,
+               0.5, 1.5, 1.5,   0,   0,
+                 0,   1,   0,   1,   1,
+                 0,   1,   0, 0.7,   0,
+               0.9, 1.3, 1.8, 1.4, 0.4), 5, 5, byrow = TRUE)
> 
> raw <- isobands(1:5, 5:1, m, levels_low = 0:1, levels_high = 1:2)
> bands <- iso_to_sfg(raw)
> 
> iso <- st_sf(
+   id = factor(1:length(bands)),
+   geometry = st_sfc(bands)
+ )
> 
> # the geometries are not valid
> st_is_valid(iso, reason = TRUE)
[1] "Self-intersection[2 2]"                   
[2] "Too few points in geometry component[4 3]"
> # this doesn't prevent us from plotting them
> ggplot(iso, aes(fill = id)) + geom_sf()
> 
> # make all geometries valid
> iso2 <- lwgeom::st_make_valid(iso)
Error in loadNamespace(name) : there is no package called ‘lwgeom’
Calls: :: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘isoband1.Rmd’ using rmarkdown
--- finished re-building ‘isoband1.Rmd’

--- re-building ‘isoband2.Rmd’ using rmarkdown
Quitting from lines 139-141 (isoband2.Rmd) 
Error: processing vignette 'isoband2.Rmd' failed with diagnostics:
there is no package called 'lwgeom'
--- failed re-building ‘isoband2.Rmd’

--- re-building ‘isoband3.Rmd’ using rmarkdown
--- finished re-building ‘isoband3.Rmd’

SUMMARY: processing the following file failed:
  ‘isoband2.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘acf.Rmd’ using rmarkdown
--- finished re-building ‘acf.Rmd’

--- re-building ‘inspect.Rmd’ using rmarkdown
Quitting from lines 101-106 (inspect.Rmd) 
Error: processing vignette 'inspect.Rmd' failed with diagnostics:
non-conformable arrays
--- failed re-building ‘inspect.Rmd’

--- re-building ‘test.Rmd’ using rmarkdown
Quitting from lines 187-200 (test.Rmd) 
Error: processing vignette 'test.Rmd' failed with diagnostics:
non-conformable arrays
--- failed re-building ‘test.Rmd’

SUMMARY: processing the following files failed:
  ‘inspect.Rmd’ ‘test.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/JavaGD.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [78s/95s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(jtools)
  > 
  > 
  > test_check("jtools")
  ── 1. Error: plot_coefs works with brms (@test-export-summs.R#294)  ────────────
  Aesthetics must be either length 1 or the same as the data (8): xmin and xmax
  Backtrace:
    1. testthat::expect_silent(print(plot_coefs(bfit1) + ggtitle("basic brms fit")))
   10. ggplot2:::print.ggplot(plot_coefs(bfit1) + ggtitle("basic brms fit"))
   12. ggplot2:::ggplot_build.ggplot(x)
   13. ggplot2:::by_layer(function(l, d) l$compute_aesthetics(d, plot))
   14. ggplot2:::f(l = layers[[i]], d = data[[i]])
   15. l$compute_aesthetics(d, plot)
   16. ggplot2:::f(..., self = self)
   17. ggplot2:::check_aesthetics(evaled, n)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 357 | SKIPPED: 0 | WARNINGS: 11 | FAILED: 1 ]
  1. Error: plot_coefs works with brms (@test-export-summs.R#294) 
  
  Error: testthat unit tests failed
  Execution halted
comp.npci: no visible global function definition for ‘qnorm’
epband.fun: no visible global function definition for ‘data’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.90’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.95’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.99’
hall.wellner.fun: no visible global function definition for ‘data’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.90’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.95’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.99’
lrt.confints: no visible global function definition for ‘qchisq’
rothman.fun: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  critical.value.hall.90 critical.value.hall.95 critical.value.hall.99
  critical.value.nair.90 critical.value.nair.95 critical.value.nair.99
  data qchisq qnorm
Consider adding
  importFrom("stats", "qchisq", "qnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘stars’
Running ‘testthat.R’ [133s/373s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(lidR)
  Loading required package: raster
  Loading required package: sp
  > 
  > options(lidR.progress = FALSE)
  > 
  > test_check("lidR")
  ── 1. Failure: catalog_apply automerge works with in memory POINTS (@test-catalo
  projection(req2) not equal to "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clrk66 +units=m +no_defs".
  1/1 mismatches
  x[1]: "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clr
  x[1]: k66 +units=m +no_defs "
  y[1]: "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clr
  y[1]: k66 +units=m +no_defs"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 971 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: catalog_apply automerge works with in memory POINTS (@test-catalog_apply-automerge.R#171) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  /data/gannet/ripley/R/test-4.1/BH/include/boost/container/detail/copy_move_algo.hpp:182:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘value_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /data/gannet/ripley/R/test-4.1/BH/include/boost/container/detail/copy_move_algo.hpp:896:16: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /data/gannet/ripley/R/test-4.1/BH/include/boost/container/detail/copy_move_algo.hpp:196:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/data/gannet/ripley/R/packages/tests-devel/lolog.Rcheck/00install.out’ for details.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/lwgeom.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'lwgeom', 'stars'
Running ‘testthat.R’ [37s/101s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mapview)
  > 
  > test_check("mapview")
  ── 1. Error: mapview() runs without any issues for stars (@test-mapview.R#477)  
  there is no package called 'stars'
  Backtrace:
   1. utils::packageVersion("stars")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 267 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: mapview() runs without any issues for stars (@test-mapview.R#477) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: 'tmaptools', 'osrm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [199s/507s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > suppressPackageStartupMessages(library(metacoder))
  > 
  > test_check("metacoder")
  ── 1. Failure: Summing counts per taxon (@test--calculations.R#103)  ───────────
  sum(x$data$tax_data$`700035949`) not equal to result$`700035949`[1].
  names for current but not for target
  
  ── 2. Failure: Summing counts per taxon (@test--calculations.R#126)  ───────────
  `total_counts` not equal to result$total[1].
  names for current but not for target
  
  ── 3. Failure: Parsing the UNITE general release fasta (@test--parsers_and_write
  result$data$tax_data$unite_seq[5] not equal to "CCAAATCATGTCTCCCGGCCGCAAGGCAGGTGCAGGCGTTTAACCCTTTGTGAACCAAAAAACCTTTCGCTTCGGCAGCAGCTCGGTTGGAGACAGCCTCTGTGTCAGCCTGCCGCTAGCACCAATTATCAAAACTTGCGGTTAGCAACATTGTCTGATTACCAAATTTTCGAATGAAAATCAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAACGCGATAGTTAATGTGAATTGCAGAATTCAGTGAATCATCGAGTCTTTGAACGCACATTGCGCCCATTGGTATTCCATTGGGCATGTCTGTTTGAGCGTCATTACAACCCTCGGTCACCACCGGTTTTGAGCGAGCAGGGTCTTCGGATCCAGCTGGCTTTAAAGTTGTAAGCTCTGCTGGCTGCTCGGCCCAACCAGAACATAGTAAAATCATGCTTGTTCAAGGTTCGCGGTCGAAGCGGTACGGCCTGAACAATACCTACCACCTCTTAGG".
  names for target but not for current
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 93 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Summing counts per taxon (@test--calculations.R#103) 
  2. Failure: Summing counts per taxon (@test--calculations.R#126) 
  3. Failure: Parsing the UNITE general release fasta (@test--parsers_and_writers.R#119) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘MIMSunit-Ex.R’ failed
The error most likely occurred in:

> ### Name: import_mhealth_csv
> ### Title: Import raw multi-channel accelerometer data stored in mHealth
> ###   Specification
> ### Aliases: import_mhealth_csv
> 
> ### ** Examples
> 
>   default_ops = options()
>   options(digits.secs=3)
>   # Use the sample mhealth csv file provided by the package
>   filepath = system.file('extdata', 'mhealth.csv', package='MIMSunit')
>   filepath
[1] "/data/gannet/ripley/R/packages/tests-devel/MIMSunit.Rcheck/MIMSunit/extdata/mhealth.csv"
> 
>   # Load the file
>   df = import_mhealth_csv(filepath)
Error: Assigned data `as.character(df[, factor_cols])` must be compatible with existing data.
✖ Existing data has 5000 rows.
✖ Assigned data has 0 rows.
ℹ Only vectors of size 1 are recycled.
Backtrace:
    █
 1. └─MIMSunit::import_mhealth_csv(filepath)
 2.   ├─base::`[<-`(`*tmp*`, , factor_cols, value = character(0))
 3.   └─tibble:::`[<-.tbl_df`(`*tmp*`, , factor_cols, value = character(0))
 4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 5.       └─tibble:::vectbl_recycle_rhs(...)
 6.         └─base::tryCatch(...)
 7.           └─base:::tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)
Execution halted
listGenoToTable: no visible binding for global variable ‘dummy’
Undefined global functions or variables:
  dummy
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/MomTrunc.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘jpndistrict’
Package required but not available: ‘lwgeom’

Package suggested but not available for checking: ‘stars’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘nws/R/zzz.R’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

blendOptions: warning in assign(names[i], new[[i]], env = options):
  partial argument match of 'env' to 'envir'
docall: warning in get(as.character(fun), env = .GlobalEnv, mode =
  "function"): partial argument match of 'env' to 'envir'
logMsg: no visible global function definition for ‘flush.console’
nwsPkgInfo: no visible global function definition for
  ‘packageDescription’
initialize,nwsServer: no visible global function definition for
  ‘make.socket’
initialize,nwsServer: no visible global function definition for
  ‘close.socket’
Undefined global functions or variables:
  close.socket flush.console make.socket packageDescription
Consider adding
  importFrom("utils", "close.socket", "flush.console", "make.socket",
             "packageDescription")
to your NAMESPACE file.
mapvar: no visible global function definition for ‘data’
mapvar: no visible binding for global variable ‘state.fips’
mapvar: no visible global function definition for ‘rgb’
mapvar: no visible global function definition for ‘rect’
mapvar: no visible global function definition for ‘text’
rowScrape: no visible global function definition for ‘tail’
rowScrape: no visible global function definition for ‘head’
scrapeTable: no visible binding for global variable ‘tail’
Undefined global functions or variables:
  data head rect rgb state.fips tail text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "rect", "text")
  importFrom("utils", "data", "head", "tail")
to your NAMESPACE file.
Running ‘testthat.R’ [39s/109s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(OpenLand)
  > 
  > test_check("OpenLand")
  ── 1. Error: Behavior of summary_map (@test_generalfunctions.R#53)  ────────────
  Assigned data `c(as.numeric(names(value_map)[i]), value_map[[i]])` must be compatible with row subscript `i`.
  ✖ 1 row must be assigned.
  ✖ Assigned data has 2 rows.
  ℹ Only vectors of size 1 are recycled.
  Backtrace:
    1. testthat::expect_silent(...)
    9. OpenLand::summary_map(...)
   11. tibble:::`[<-.tbl_df`(`*tmp*`, i, c(1:2), value = c(1, 1983))
   12. tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   13. tibble:::vectbl_recycle_rhs(...)
   14. base::tryCatch(...)
   15. base:::tryCatchList(expr, classes, parentenv, handlers)
   16. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   17. value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 112 | SKIPPED: 0 | WARNINGS: 24 | FAILED: 1 ]
  1. Error: Behavior of summary_map (@test_generalfunctions.R#53) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘palr-Ex.R’ failed
The error most likely occurred in:

> ### Name: image_pal
> ### Title: Map data values to colours
> ### Aliases: image_pal image_raster image_stars
> 
> ### ** Examples
> 
> set.seed(28)
> vals <- sort(rnorm(100))
> cols <- image_pal(vals, zlim = c(-2.4, 2))
> plot(vals, col = cols); abline(h = 2)
> points(vals, pch  = 19, cex = 0.1) ## zlim excluded some of the range
> if (requireNamespace("raster", quietly = TRUE)) {
+ im <- image_raster(volcano)
+ library(raster)
+ plotRGB(im)
+ }
Loading required package: sp
Warning in .couldBeLonLat(x, warnings = warnings) :
  CRS is NA. Assuming it is longitude/latitude
> if (!requireNamespace("stars", quietly = TRUE)) {
+ library(stars)
+ x <- st_as_stars(volcano)
+ plot(image_stars(x), rgb = 1:3)
+ }
Error in library(stars) : there is no package called ‘stars’
Execution halted
Package required but not available: ‘stplanr’

Package suggested but not available for checking: ‘tmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘test-async.R’ [23s/29s]
  Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pkgcache)
  > 
  > test_check("pkgcache")
  ── 1. Error: load_primary_pkgs (@test-metadata-cache.R#191)  ───────────────────
  No metadata available
  Backtrace:
   1. pkgcache:::synchronise(get_private(cmc)$load_primary_pkgs(oneday()))
   2. get_private(cmc)$load_primary_pkgs(oneday())
   3. pkgcache:::cmc__load_primary_pkgs(self, private, max_age)
   4. private$update_replica_rds(alert = FALSE)
   5. pkgcache:::cmc__update_replica_rds(self, private, alert)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 305 | SKIPPED: 28 | WARNINGS: 2 | FAILED: 1 ]
  1. Error: load_primary_pkgs (@test-metadata-cache.R#191) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: `data_frame()` is deprecated as of tibble 1.1.0.
See ‘/data/gannet/ripley/R/packages/tests-devel/poio.Rcheck/00install.out’ for details.
Package required but not available: ‘tmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘run-all.R’ [11s/25s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("ProjectTemplate")
  Loading required package: ProjectTemplate
  ── 1. Failure: Custom configuration is added to config (@test-add_config.R#12)  
  `load.project()` generated warnings:
  * 'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
  
  ✔ |  OK F W S | Context
  
  ⠏ |   0       | Example tests
  ✔ |   1       | Example tests
  
  ══ Results ═════════════════════════════════════════════════════════════════════
  OK:       1
  Failed:   0
  Warnings: 0
  Skipped:  0
  
  Way to go!
  ✔ |  OK F W S | Context
  
  ⠏ |   0       | Example tests
  ✔ |   1       | Example tests
  
  ══ Results ═════════════════════════════════════════════════════════════════════
  OK:       1
  Failed:   0
  Warnings: 0
  Skipped:  0
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] TRUE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 852 | SKIPPED: 4 | WARNINGS: 281 | FAILED: 1 ]
  1. Failure: Custom configuration is added to config (@test-add_config.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  /data/gannet/ripley/R/packages/tests-devel/qtbase/src/EventLoop.cpp:103:12: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
  /data/gannet/ripley/R/packages/tests-devel/qtbase/src/EventLoop.cpp:92:7: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/qtbase.Rcheck/00install.out’ for details.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘compileMetaObject’
Found the following file(s) containing GNU extensions:
  src-build/Makefile
  tools/kdebindings-build/Makefile
  tools/kdebindings-build/generator/Makefile
  tools/kdebindings-build/generator/generators/Makefile
  tools/kdebindings-build/generator/generators/dump/Makefile
  tools/kdebindings-build/generator/generators/smoke/Makefile
  tools/kdebindings-build/generator/parser/Makefile
  tools/kdebindings-build/smoke/Makefile
  tools/kdebindings-build/smoke/qt/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable
packages’ in the ‘Writing R Extensions’ manual.
File ‘qtbase/libs/qtbase.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘Rf_EncodeInteger’,
    ‘Rf_EncodeLogical’, ‘Rf_EncodeReal’, ‘Rf_formatInteger’,
    ‘Rf_formatLogical’, ‘Rf_formatReal’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: information on .o files is not available
File ‘qtpaint/libs/qtpaint.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘batchelor’
.disableThreads: no visible global function definition for
  ‘stopCluster’
.enableThreads: no visible global function definition for ‘detectCores’
.enableThreads: no visible global function definition for
  ‘makePSOCKcluster’
.enableThreads: no visible global function definition for
  ‘clusterExport’
.enableThreads: no visible global function definition for ‘clusterCall’
.forwardSelection: no visible binding for global variable ‘var’
.forwardSelection: no visible global function definition for ‘glm’
.forwardSelection: no visible global function definition for ‘formula’
.forwardSelection: no visible global function definition for ‘binomial’
.forwardSelection: no visible global function definition for ‘lm’
.forwardSelection: no visible global function definition for ‘predict’
.predict.internal: no visible global function definition for ‘predict’
randomGLM: no visible binding for global variable ‘cor’
randomGLM: no visible binding for global variable ‘sd’
randomGLM: no visible global function definition for ‘var’
thinRandomGLM: no visible global function definition for ‘glm’
thinRandomGLM: no visible global function definition for ‘binomial’
thinRandomGLM: no visible global function definition for ‘lm’
Undefined global functions or variables:
  binomial clusterCall clusterExport cor detectCores formula glm lm
  makePSOCKcluster predict sd stopCluster var
Consider adding
  importFrom("stats", "binomial", "cor", "formula", "glm", "lm",
             "predict", "sd", "var")
to your NAMESPACE file.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-devel/Rblpapi.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [28s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("RCzechia")
  Loading required package: RCzechia
  Loading required package: sf
  Linking to GEOS 3.7.1, GDAL 2.3.2, PROJ 5.2.0
  ── 1. Error: (unknown) (@test-2-code.R#20)  ────────────────────────────────────
  lwgeom required: install that first
  Backtrace:
    1. RCzechia::casti()
    9. RCzechia::union_sf(., "NAZ_OBEC")
    3. data[vec, ]
   10. sf::st_make_valid(.)
   21. sf:::st_make_valid.sfc(st_geometry(x))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 145 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test-2-code.R#20) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘vignette.Rmd’ using rmarkdown
Loading required package: sf
Linking to GEOS 3.7.1, GDAL 2.3.2, PROJ 5.2.0

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

RCzechia: downloading remote dataset.
RCzechia: downloading remote dataset.
udunits system database from /usr/share/udunits
RCzechia: downloading remote dataset.
Quitting from lines 109-125 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
lwgeom required: install first?
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  bits.c:1247:23: warning: array subscript 8 is outside array bounds of ‘unsigned int[1]’ [-Warray-bounds]
  bits.c:1265:18: warning: array subscript 9 is outside array bounds of ‘unsigned int[1]’ [-Warray-bounds]
See ‘/data/gannet/ripley/R/packages/tests-devel/RDieHarder.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd’ using rmarkdown
Loading required package: rJava
Loading required package: Rdroolsjars

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: 'purrr'

The following object is masked from 'package:magrittr':

    set_names

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
Quitting from lines 183-187 (Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd) 
Error: processing vignette 'Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd' failed with diagnostics:
Assigned data `paste(seq(as.numeric(lowerRange), as.numeric(upperRange)), collapse = ",")` must be compatible with existing data.
ℹ Error occurred for column `Indices`.
✖ No common type for `value` <character> and `x` <double>.
--- failed re-building ‘Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd’

SUMMARY: processing the following file failed:
  ‘Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd’

Error: Vignette re-building failed.
Execution halted
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.
Running ‘testthat.R’ [5s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(riskclustr)
  > 
  > test_check("riskclustr")
  ── 1. Error: optimal_kmeans_d prints message if no seed is set (@test-optimal_km
  `i` must have one dimension, not 2.
  Backtrace:
    1. testthat::expect_message(...)
    6. riskclustr::optimal_kmeans_d(...)
    7. base::lapply(...)
    8. riskclustr:::FUN(X[[i]], ...)
    9. riskclustr::d(label = "cls", M = M, factors = factors, data = temp)
   12. tibble:::`[.tbl_df`(data, data[, label] == 0, )
   13. tibble:::tbl_subset_row(xo, i = i, i_arg)
   14. tibble:::vectbl_as_row_index(i, x, i_arg)
   15. tibble:::vectbl_as_row_location(i, nr, i_arg, assign)
   22. vctrs::vec_as_location(i, n, arg = as_label(i_arg))
  
  ── 2. Error: optimal_kmeans_d returns expected optimal_d value (@test-optimal_km
  `i` must have one dimension, not 2.
  Backtrace:
    1. testthat::expect_equal(...)
    4. riskclustr::optimal_kmeans_d(...)
    5. base::lapply(...)
    6. riskclustr:::FUN(X[[i]], ...)
    7. riskclustr::d(label = "cls", M = M, factors = factors, data = temp)
   10. tibble:::`[.tbl_df`(data, data[, label] == 0, )
   11. tibble:::tbl_subset_row(xo, i = i, i_arg)
   12. tibble:::vectbl_as_row_index(i, x, i_arg)
   13. tibble:::vectbl_as_row_location(i, nr, i_arg, assign)
   20. vctrs::vec_as_location(i, n, arg = as_label(i_arg))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 26 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 2 ]
  1. Error: optimal_kmeans_d prints message if no seed is set (@test-optimal_kmeans_d.R#49) 
  2. Error: optimal_kmeans_d returns expected optimal_d value (@test-optimal_kmeans_d.R#65) 
  
  Error: testthat unit tests failed
  Execution halted
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/rJava.Rcheck/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:
  graph_io_chac.c:106:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  graph_io_chac.c:179:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  graph_io_chac.c:208:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/rmumps.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rserv.c:2150:3: warning: ‘RSA_generate_key’ is deprecated [-Wdeprecated-declarations]
  Rserv.c:816:4: warning: ignoring return value of ‘setgid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:817:3: warning: ignoring return value of ‘setuid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:820:22: warning: ignoring return value of ‘setgid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:821:22: warning: ignoring return value of ‘setuid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:372:2: warning: ignoring return value of ‘chown’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:375:3: warning: ignoring return value of ‘chown’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:2342:3: warning: ignoring return value of ‘chdir’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:3351:4: warning: ignoring return value of ‘chdir’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:3358:3: warning: ignoring return value of ‘chdir’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:2088:7: warning: ignoring return value of ‘setgid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:2090:7: warning: ignoring return value of ‘setuid’, declared with attribute warn_unused_result [-Wunused-result]
  oc.c:47:5: warning: ‘RAND_pseudo_bytes’ is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-devel/Rserve.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor 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.
Math.Sym: no visible binding for global variable ‘transtab’
jythonStart: no visible global function definition for ‘.jinit’
jythonStart: no visible global function definition for ‘.jnew’
jythonStart: no visible binding for global variable ‘.Jython’
sympy: no visible binding for global variable ‘.Jython’
sympy: no visible global function definition for ‘.jstrVal’
sympyStart: no visible binding for global variable ‘.Jython’
Undefined global functions or variables:
  .Jython .jinit .jnew .jstrVal transtab
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-devel/RVowpalWabbit.Rcheck/00install.out’ for details.
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.
Packages suggested but not available for checking:
  'loomR', 'SDMTools', 'MAST', 'monocle'
Packages suggested but not available for checking:
  'lwgeom', 'stars', 'tmap'
Running examples in ‘sf-Ex.R’ failed
The error most likely occurred in:

> ### Name: geos_measures
> ### Title: Compute geometric measurements
> ### Aliases: geos_measures st_area st_length st_distance
> 
> ### ** Examples
> 
> b0 = st_polygon(list(rbind(c(-1,-1), c(1,-1), c(1,1), c(-1,1), c(-1,-1))))
> b1 = b0 + 2
> b2 = b0 + c(-0.2, 2)
> x = st_sfc(b0, b1, b2)
> st_area(x)
[1] 4 4 4
> line = st_sfc(st_linestring(rbind(c(30,30), c(40,40))), crs = 4326)
> st_length(line)
Error in st_length(line) : 
  package lwgeom required, please install it first
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘sf1.Rmd’ using rmarkdown
Quitting from lines 795-797 (sf1.Rmd) 
Error: processing vignette 'sf1.Rmd' failed with diagnostics:
package lwgeom required, please install it first
--- failed re-building ‘sf1.Rmd’

--- re-building ‘sf2.Rmd’ using rmarkdown
--- finished re-building ‘sf2.Rmd’

--- re-building ‘sf3.Rmd’ using rmarkdown
--- finished re-building ‘sf3.Rmd’

--- re-building ‘sf4.Rmd’ using rmarkdown
--- finished re-building ‘sf4.Rmd’

--- re-building ‘sf5.Rmd’ using rmarkdown
Quitting from lines 208-210 (sf5.Rmd) 
Error: processing vignette 'sf5.Rmd' failed with diagnostics:
there is no package called 'tmap'
--- failed re-building ‘sf5.Rmd’

--- re-building ‘sf6.Rmd’ using rmarkdown
--- finished re-building ‘sf6.Rmd’

SUMMARY: processing the following files failed:
  ‘sf1.Rmd’ ‘sf5.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'chromVAR', 'TFBSTools', 'motifmatchr', 'EnsDb.Hsapiens.v75',
  'JASPAR2018'
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(simrel)
  > 
  > test_check("simrel")
  ── 1. Error: Prepare Design (@test-utils.R#44)  ────────────────────────────────
  Can't join on 'q' x 'q' because of incompatible types (list / list)
  Backtrace:
   1. testthat::expect_identical(prepare_design(opts), dgn)
   3. testthat:::compare.default(act$val, exp$val)
   5. dplyr:::all.equal.tbl_df(x, y, ...)
   6. dplyr:::equal_data_frame(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 169 | SKIPPED: 21 | WARNINGS: 3 | FAILED: 1 ]
  1. Error: Prepare Design (@test-utils.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘smoothr-Ex.R’ failed
The error most likely occurred in:

> ### Name: drop_crumbs
> ### Title: Remove small polygons or line segments
> ### Aliases: drop_crumbs
> 
> ### ** Examples
> 
> # remove polygons smaller than 200km2
> p <- jagged_polygons$geometry[7]
> area_thresh <- units::set_units(200, km^2)
> p_dropped <- drop_crumbs(p, threshold = area_thresh)
Error in st_area.sfc(x[1]) : 
  package lwgeom required, please install it first
Calls: drop_crumbs ... set_units.numeric -> as_units -> units -> size_fxn -> st_area.sfc
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘smoothr.Rmd’ using rmarkdown
Loading required package: sp
Linking to GEOS 3.7.1, GDAL 2.3.2, PROJ 5.2.0
udunits system database from /usr/share/udunits

Attaching package: 'smoothr'

The following object is masked from 'package:stats':

    smooth

Quitting from lines 209-215 (smoothr.Rmd) 
Error: processing vignette 'smoothr.Rmd' failed with diagnostics:
package lwgeom required, please install it first
--- failed re-building ‘smoothr.Rmd’

SUMMARY: processing the following file failed:
  ‘smoothr.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘SpatialKDE.Rmd’ using rmarkdown
Linking to GEOS 3.7.1, GDAL 2.3.2, PROJ 5.2.0

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 26-31 (SpatialKDE.Rmd) 
Error: processing vignette 'SpatialKDE.Rmd' failed with diagnostics:
there is no package called 'tmap'
--- failed re-building ‘SpatialKDE.Rmd’

SUMMARY: processing the following file failed:
  ‘SpatialKDE.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘spatial.tools-Ex.R’ failed
The error most likely occurred in:

> ### Name: tahoe_highrez_training
> ### Title: Point and polygon files for use with spatial.tools
> ### Aliases: tahoe_highrez_training
> ### Keywords: data
> 
> ### ** Examples
> 
> library("raster")
Loading required package: sp
> library("rgdal")
rgdal: version: 1.4-8, (SVN revision 845)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.3.2, released 2018/09/21
 Path to GDAL shared files: /usr/share/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 5.2.0, September 15th, 2018, [PJ_VERSION: 520]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.4-1 
> tahoe_highrez_training_polygons <- readOGR(
+ 	dsn=system.file("external", package="spatial.tools"),layer="tahoe_highrez_training")
OGR data source with driver: ESRI Shapefile 
Source: "/data/gannet/ripley/R/packages/tests-devel/spatial.tools.Rcheck/spatial.tools/external", layer: "tahoe_highrez_training"
with 8 features
It has 2 fields
> spplot(tahoe_highrez_training_polygons,zcol="Class")
Warning in extend.limits(range(as.numeric(z), finite = TRUE)) :
  NAs introduced by coercion
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 seq.default(zrng[1], zrng[2], length.out = cuts + 2) : 
  'from' must be a finite number
Calls: spplot ... <Anonymous> -> levelplot.formula -> seq -> seq.default
Execution halted
Running ‘testthat.R’ [15s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(spsurvey)
  Loading required package: sf
  Linking to GEOS 3.7.1, GDAL 2.3.2, PROJ 5.2.0
  Loading required package: sp
  
  Version 4.1.0 of the spsurvey package was loaded successfully.
  
  > 
  > test_check("spsurvey")
  
  Stratum: None 
  Current number of levels: 2 
  Current number of levels: 3 
  Current number of levels: 4 
  Final number of levels: 4 
  
  Stratum: None 
  Current number of levels: 2 
  Current number of levels: 3 
  Current number of levels: 4 
  Final number of levels: 4 
  
  Stratum: None 
  Current number of levels: 2 
  Current number of levels: 3 
  Current number of levels: 4 
  Final number of levels: 4 
  
  Stratum: None 
  Current number of levels: 2 
  Current number of levels: 3 
  Final number of levels: 3 
  
  Stratum: LAKE/POND 
  Current number of levels: 2 
  Current number of levels: 4 
  Final number of levels: 4 
  
  Stratum: RESERVOIR 
  Current number of levels: 2 
  Current number of levels: 3 
  Current number of levels: 4 
  Current number of levels: 5 
  Current number of levels: 6 
  Final number of levels: 6 
  
  Stratum: None 
  Current number of levels: 2 
  Current number of levels: 3 
  Final number of levels: 3 
  
  Stratum: None 
  Current number of levels: 2 
  Current number of levels: 4 
  Current number of levels: 5 
  Current number of levels: 6 
  Final number of levels: 6 
  ── 1. Error: (unknown) (@test-grts.R#107)  ─────────────────────────────────────
  package lwgeom required, please install it first
  Backtrace:
   1. spsurvey::grts(...)
   2. sf::st_length(sf.object)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 28 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test-grts.R#107) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [28s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > #    Copyright 2015 Province of British Columbia
  > #
  > #    Licensed under the Apache License, Version 2.0 (the "License");
  > #    you may not use this file except in compliance with the License.
  > #    You may obtain a copy of the License at
  > #
  > #       http://www.apache.org/licenses/LICENSE-2.0
  > #
  > #    Unless required by applicable law or agreed to in writing, software
  > #    distributed under the License is distributed on an "AS IS" BASIS,
  > #    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  > #    See the License for the specific language governing permissions and
  > #    limitations under the License.
  > 
  > library(testthat)
  > library(ssdtools)
  
  Attaching package: 'ssdtools'
  
  The following objects are masked from 'package:stats':
  
      dgamma, dweibull, pgamma, pweibull, qgamma, qweibull, rgamma,
      rweibull
  
  > 
  > test_check("ssdtools")
  ── 1. Failure: ssd_gof fitdistscens (@test-gof.R#46)  ──────────────────────────
  as.data.frame(ssd_gof(fluazinam_dists)) not equal to structure(...).
  Attributes: < Component "row.names": Modes: numeric, character >
  Attributes: < Component "row.names": target is numeric, current is character >
  
  ── 2. Failure: manual (@test-schwarz-tillmans.R#24)  ───────────────────────────
  as.data.frame(ssd_gof(dists)) not equal to structure(...).
  Attributes: < Component "row.names": Modes: numeric, character >
  Attributes: < Component "row.names": target is numeric, current is character >
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 269 | SKIPPED: 0 | WARNINGS: 12 | FAILED: 2 ]
  1. Failure: ssd_gof fitdistscens (@test-gof.R#46) 
  2. Failure: manual (@test-schwarz-tillmans.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘lwgeom’

Package suggested but not available for checking: ‘starsdata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'tmap', 'pct'
Package required but not available: ‘lwgeom’

Packages suggested but not available for checking: 'pct', 'tmap', 'osrm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [32s/55s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(taxa)
  
  Attaching package: 'taxa'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  > 
  > test_check("taxa")
  ── 1. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers
  test_obj$data$my_data$taxon_id not equal to c("j", "i").
  names for target but not for current
  
  ── 2. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers
  test_obj$data$my_data$taxon_id not equal to c("j", "i").
  names for target but not for current
  
  ── 3. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers
  test_obj$data$my_data$taxon_id not equal to c("j", "i").
  names for target but not for current
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 607 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers.R#52) 
  2. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers.R#56) 
  3. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers.R#60) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘tmaptools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [21s/53s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidytext)
  > 
  > test_check("tidytext")
  ── 1. Failure: Can tidy corpus from tm package (@test-corpus-tidiers.R#15)  ────
  paste(as.character(ovid[[1]]), collapse = " ") not equal to td$text[1].
  names for current but not for target
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 297 | SKIPPED: 1 | WARNINGS: 2 | FAILED: 1 ]
  1. Failure: Can tidy corpus from tm package (@test-corpus-tidiers.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: 'tmaptools', 'stars'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lwgeom', 'stars'

Package suggested but not available for checking: ‘tmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/tolBasis.Rcheck/00install.out’ for details.
File ‘tpr/libs/tpr.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’
File ‘tpr/libs/tpr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘moveVis’
Package unavailable to check Rd xrefs: ‘moveVis’
Running examples in ‘Traitspace-Ex.R’ failed
The error most likely occurred in:

> ### Name: Traitspace
> ### Title: Traitspace Model
> ### Aliases: Traitspace
> 
> ### ** Examples
> 
> data(spdata)
> species<-spdata$species  #species column
> trt<-cbind(spdata$t1,spdata$t2) #two traits
> env<-spdata$env     #one env gradient
> site<-spdata$site   #site information
> result1<-Traitspace(species, trt, env, site)
Error: $ operator is invalid for atomic vectors
Execution halted
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/tricolore.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘Demo.Rmd’ using rmarkdown
Quitting from lines 65-76 (Demo.Rmd) 
Error: processing vignette 'Demo.Rmd' failed with diagnostics:
package lwgeom required, please install it first
--- failed re-building ‘Demo.Rmd’

SUMMARY: processing the following file failed:
  ‘Demo.Rmd’

Error: Vignette re-building failed.
Execution halted
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.
Running ‘testthat.R’ [18s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > library("wyz.code.metaTesting")
  > test_check("wyz.code.metaTesting")
  ── 1. Failure: computeArgumentsCombination (@test_computeArgumentsCombination.R#
  `d` not equal to ex[3].
  1/1 mismatches
  [1] 3 - 2 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 490 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: computeArgumentsCombination (@test_computeArgumentsCombination.R#47) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-devel/x13binary.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘lubridate::intersect’ by ‘raster::intersect’ when loading ‘xROI’
  Warning: replacing previous import ‘lubridate::union’ by ‘raster::union’ when loading ‘xROI’
See ‘/data/gannet/ripley/R/packages/tests-devel/xROI.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
Running examples in 'abn-Ex.R' failed
The error most likely occurred in:

> ### Name: plotabn
> ### Title: Plot an ABN graphic
> ### Aliases: plotabn
> ### Keywords: models hplot
> 
> ### ** Examples
> 
> #Define distribution list
> dist <- list(a="gaussian", b="gaussian", c="gaussian", d="gaussian", e="binomial", f="binomial")
> 
> #Define a matrix formulation
> arc.strength <- matrix(c(0,0.5,0.5,0.7,0.1,0,
+                               0,0,0.3,0.1,0,0.8,
+                               0,0,0,0.35,0.66,0,
+                               0,0,0,0,0.9,0,
+                               0,0,0,0,0,0.8,
+                               0,0,0,0,0,0),nrow = 6L, ncol = 6L, byrow = TRUE)
> 
> #Naming of the matrix
> colnames(arc.strength) <- rownames(arc.strength) <- names(dist)
> 
> #Plot from a formula
> plotabn(dag.m = ~a|b:c:e+b|c:d:f+e|f, data.dist = dist)
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plotabn ... <Anonymous> -> <Anonymous> -> plot.default -> xy.coords
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/AbsFilterGSEA.Rcheck/00install.out' for details.
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    R  14.6Mb
Error(s) in re-building vignettes:
--- re-building 'ActiveDriverWGSR.Rmd' using rmarkdown
Quitting from lines 109-116 (ActiveDriverWGSR.Rmd) 
Error: processing vignette 'ActiveDriverWGSR.Rmd' failed with diagnostics:
.onLoad failed in loadNamespace() for 'S4Vectors', details:
  call: validObject(.Object)
  error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
--- failed re-building 'ActiveDriverWGSR.Rmd'

SUMMARY: processing the following file failed:
  'ActiveDriverWGSR.Rmd'

Error: Vignette re-building failed.
Execution halted
asp: no visible global function definition for 'as.formula'
asp: no visible global function definition for 'var'
aspm: no visible binding for global variable 'X.Declan'
aspm: no visible binding for global variable 'Z.Jaida'
aspm: no visible binding for global variable 'group.vec.Handan'
aspm: no visible global function definition for 'as.formula'
aspm: no visible global function definition for 'glm'
aspm: no visible global function definition for 'binomial'
aspm: no visible global function definition for 'poisson'
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/adaptiveGPCA.Rcheck/00install.out' for details.
Running examples in 'ADAPTS-Ex.R' failed
The error most likely occurred in:

> ### Name: estCellPercent.proportionsInAdmixture
> ### Title: WGCNA::proportionsInAdmixture deconvolution
> ### Aliases: estCellPercent.proportionsInAdmixture
> 
> ### ** Examples
> 
> #This toy example 
> library(ADAPTS)
> fullLM22 <- ADAPTS::LM22[1:30, 1:4]
> smallLM22 <- fullLM22[1:25,] 
> 
> cellEst <- estCellPercent.proportionsInAdmixture(refExpr=smallLM22, geneExpr=fullLM22)
Error: .onLoad failed in loadNamespace() for 'S4Vectors', details:
  call: validObject(.Object)
  error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.7Mb
    pictures   2.1Mb
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    data  20.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/aliases2entrez.Rcheck/00install.out' for details.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    data  15.6Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Running examples in 'anchoredDistr-Ex.R' failed
The error most likely occurred in:

> ### Name: plotMAD
> ### Title: Plot the data contained in MADproject object slots.
> ### Aliases: plotMAD plotMAD,MADproject,ANY-method
> ###   plotMAD,MADproject,character-method
> 
> ### ** Examples
> 
> data(pumping)
> plotMAD(pumping, "realizations")
Error: Assigned data `x@observations` must be compatible with existing data.
x Existing data has 300 rows.
x Assigned data has 100 rows.
i Only vectors of size 1 are recycled.
Backtrace:
     x
  1. +-anchoredDistr::plotMAD(pumping, "realizations")
  2. \-anchoredDistr::plotMAD(pumping, "realizations")
  3.   +-base::`$<-`(...)
  4.   \-tibble:::`$<-.tbl_df`(...)
  5.     \-tibble:::tbl_subassign(...)
  6.       \-tibble:::vectbl_recycle_rhs(...)
  7.         \-base::tryCatch(...)
  8.           \-base:::tryCatchList(expr, classes, parentenv, handlers)
  9.             \-base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 10.               \-value[[3L]](cond)
Execution halted
Error(s) in re-building vignettes:
--- re-building 'anchoredDistr.Rmd' using rmarkdown
Quitting from lines 85-86 (anchoredDistr.Rmd) 
Error: processing vignette 'anchoredDistr.Rmd' failed with diagnostics:
Assigned data `x@observations` must be compatible with existing data.
x Existing data has 300 rows.
x Assigned data has 100 rows.
i Only vectors of size 1 are recycled.
--- failed re-building 'anchoredDistr.Rmd'

SUMMARY: processing the following file failed:
  'anchoredDistr.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs     4.2Mb
annot : annotlist: no visible global function definition for
  'read.table'
annot : annotlist: no visible global function definition for
  'write.table'
annot: no visible global function definition for 'flush.console'
annot: no visible global function definition for 'read.table'
annot: no visible global function definition for 'choose.dir'
Undefined global functions or variables:
  choose.dir flush.console read.table write.table
Consider adding
  importFrom("utils", "choose.dir", "flush.console", "read.table",
             "write.table")
to your NAMESPACE file.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   1.8Mb
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(aoos)
  > 
  > test_check("aoos")
  -- 1. Failure: Type inheritance (@test-S4-types.R#75)  -------------------------
  inherits(Child(), "Test2") isn't true.
  
  -- 2. Failure: Type with VIRTUAL (@test-S4-types.R#111)  -----------------------
  names(Test(x = 2)) == "x" isn't true.
  
  -- 3. Failure: Type with VIRTUAL (@test-S4-types.R#112)  -----------------------
  inherits(Test(), "Type") isn't true.
  
  == testthat results  ===========================================================
  [ OK: 187 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Type inheritance (@test-S4-types.R#75) 
  2. Failure: Type with VIRTUAL (@test-S4-types.R#111) 
  3. Failure: Type with VIRTUAL (@test-S4-types.R#112) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(apa)
  > 
  > test_check("apa")
  -- 1. Error: Output for anova_apa: repeated-measures ANOVA (@test-anova-apa.R#13
  Assigned data `<list>` must be compatible with existing data.
  i Error occurred for column `df_n`.
  x No common type for `value` <character> and `x` <double>.
  Backtrace:
    1. apa::anova_apa(...)
    2. apa:::anova_apa_afex(x, effect, sph_corr, es, format, info, print)
    7. tibble:::`[<-.tbl_df`(...)
    8. tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    9. tibble:::tbl_subassign_row(xj, i, value, value_arg)
   10. base::tryCatch(...)
   11. base:::tryCatchList(expr, classes, parentenv, handlers)
   12. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   13. value[[3L]](cond)
  
  -- 2. Error: Output for anova_apa: factorial repeated-measures ANOVA (@test-anov
  Assigned data `<list>` must be compatible with existing data.
  i Error occurred for column `df_n`.
  x No common type for `value` <character> and `x` <double>.
  Backtrace:
    1. apa::anova_apa(...)
    2. apa:::anova_apa_afex(x, effect, sph_corr, es, format, info, print)
    7. tibble:::`[<-.tbl_df`(...)
    8. tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    9. tibble:::tbl_subassign_row(xj, i, value, value_arg)
   10. base::tryCatch(...)
   11. base:::tryCatchList(expr, classes, parentenv, handlers)
   12. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   13. value[[3L]](cond)
  
  == testthat results  ===========================================================
  [ OK: 105 | SKIPPED: 0 | WARNINGS: 9 | FAILED: 2 ]
  1. Error: Output for anova_apa: repeated-measures ANOVA (@test-anova-apa.R#135) 
  2. Error: Output for anova_apa: factorial repeated-measures ANOVA (@test-anova-apa.R#181) 
  
  Error: testthat unit tests failed
  Execution halted