'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 ‘plot’
drawGraph: no visible global function definition for ‘segments’
drawGraph: no visible global function definition for ‘lines’
drawGraph: no visible global function definition for ‘text’
drawGraph: no visible global function definition for ‘dev.off’
drugRank: no visible global function definition for ‘aggregate’
floating2: no visible global function definition for ‘cor’
timma: no visible global function definition for ‘median’
timma: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  aggregate cor dev.off lines median par pdf plot segments text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "segments", "text")
  importFrom("stats", "aggregate", "cor", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Non-standard files/directories found at top level:
  ‘DESCRIPTION.orig’ ‘README.rst’
tipom.car: no visible global function definition for ‘abline’
tipom.car: no visible global function definition for ‘axis’
tipom.heat: no visible global function definition for ‘image’
tipom.heat: no visible global function definition for ‘gray’
tipom.lw: no visible global function definition for ‘plot’
tipom.lw: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis gray image plot
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "image", "plot")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘boot’ ‘lattice’ ‘splines’ ‘tcltk’
  Please remove these calls from your code.
ls.tree: no visible global function definition for ‘lm’
ls.tree: no visible global function definition for ‘coef’
Undefined global functions or variables:
  coef lm
Consider adding
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
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.
search_collection: no visible global function definition for
  ‘URLencode’
search_company: no visible global function definition for ‘URLencode’
search_keyword: no visible global function definition for ‘URLencode’
search_list: no visible global function definition for ‘URLencode’
search_movie: no visible global function definition for ‘URLencode’
search_multi: no visible global function definition for ‘URLencode’
search_person: no visible global function definition for ‘URLencode’
search_tv: no visible global function definition for ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
extractContentDOM: no visible global function definition for
  ‘capture.output’
extractHTMLStrip: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Package suggested but not available for checking: ‘corpus.JSS.papers’
Tosls.formula: no visible global function definition for ‘model.matrix’
Tosls.formula: no visible global function definition for
  ‘model.response’
summary: no visible global function definition for ‘coef’
summary: no visible global function definition for ‘pt’
Undefined global functions or variables:
  coef model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘Cairo’ ‘RGtk2’ ‘colorspace’ ‘gWidgets’ ‘tourr’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘TeachingDemos’ ‘ash’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Cairo’ ‘RGtk2’ ‘colorspace’ ‘gWidgets’ ‘tourr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ConfA: no visible global function definition for ‘qf’
EstM2Sn: no visible global function definition for ‘nlm’
EstM2Sn: no visible global function definition for ‘qnorm’
TV.model: no visible global function definition for ‘dev.new’
TV.model: no visible global function definition for ‘points’
betaBino: no visible global function definition for ‘pbinom’
doseD: no visible global function definition for ‘lm’
doseD: no visible global function definition for ‘dev.new’
doseD: no visible global function definition for ‘par’
doseD: no visible global function definition for ‘plot’
doseD: no visible global function definition for ‘axTicks’
doseD: no visible global function definition for ‘axis’
doseD: no visible global function definition for ‘lines’
doseD: no visible global function definition for ‘abline’
doseD: no visible global function definition for ‘legend’
setD: no visible global function definition for ‘dev.new’
setD: no visible global function definition for ‘par’
setD: no visible global function definition for ‘pbinom’
setD: no visible global function definition for ‘abline’
setD: no visible global function definition for ‘axis’
setD: no visible global function definition for ‘rect’
setD: no visible global function definition for ‘lines’
setD: no visible global function definition for ‘text’
setD: no visible global function definition for ‘axTicks’
setD: no visible global function definition for ‘legend’
spoD : spoD_A: no visible global function definition for ‘chisq.test’
Undefined global functions or variables:
  abline axTicks axis chisq.test dev.new legend lines lm nlm par pbinom
  plot points qf qnorm rect text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axTicks", "axis", "legend", "lines",
             "par", "plot", "points", "rect", "text")
  importFrom("stats", "chisq.test", "lm", "nlm", "pbinom", "qf", "qnorm")
to your NAMESPACE file.
align1d : obj: no visible global function definition for ‘dist’
align2d : obj: no visible global function definition for ‘dist’
align2d : pen: no visible global function definition for ‘dist’
align2d: no visible global function definition for ‘dist’
sumt: no visible global function definition for ‘optim’
tpe1d: no visible global function definition for ‘hclust’
tpe2d: no visible global function definition for ‘hclust’
tpe2d: no visible global function definition for ‘cmdscale’
Undefined global functions or variables:
  cmdscale dist hclust optim
Consider adding
  importFrom("stats", "cmdscale", "dist", "hclust", "optim")
to your NAMESPACE file.
Found the following significant warnings:
  RngStream.c:347:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TPmsm.Rcheck/00install.out’ for details.
Package in Depends field not imported from: ‘lgtdl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ci.plot: no visible global function definition for ‘gaussian’
ci.plot: no visible global function definition for ‘qnorm’
ci.plot: no visible global function definition for ‘plot’
ci.plot: no visible global function definition for ‘lines’
cst.fit.ff: no visible global function definition for ‘pnorm’
cstfit.1: no visible global function definition for ‘var’
gof.test.boots.pf: no visible binding for global variable ‘sd’
gof.test.int.1.ff: no visible global function definition for ‘quantile’
gof.test.int.1.ff: no visible global function definition for ‘var’
gof.test.int.ff: no visible global function definition for ‘pnorm’
gofTest: no visible binding for global variable ‘sd’
plotGof: no visible global function definition for ‘plot’
plotGof : <anonymous>: no visible global function definition for
  ‘lines’
plotGof: no visible global function definition for ‘lines’
sig.test.int.1.ff: no visible global function definition for ‘quantile’
sig.test.int.1.ff: no visible global function definition for ‘var’
sig.test.int.ff: no visible global function definition for ‘pnorm’
test.boots.1: no visible binding for global variable ‘sd’
tpr: no visible global function definition for ‘poisson’
tpr: no visible global function definition for ‘glm.fit’
tpr: no visible global function definition for ‘coef’
tpr: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx coef gaussian glm.fit lines plot pnorm poisson qnorm quantile
  sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "approx", "coef", "gaussian", "glm.fit", "pnorm",
             "poisson", "qnorm", "quantile", "sd", "var")
to your NAMESPACE file.
Rd file 'ci.plot.Rd':
  \usage lines wider than 90 characters:
     ci.plot(x, y, se, level = 0.95, ylim = NULL, newplot = TRUE, fun = gaussian()$linkinv, dfun = gaussian()$mu.eta, ...)

These lines will be truncated in the PDF manual.
File ‘tpr/libs/tpr.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’

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’.
DeadReckoning: no visible global function definition for ‘filter’
DeadReckoning: no visible global function definition for ‘approx’
DeadReckoning: no visible global function definition for ‘lm’
Mapper: no visible global function definition for ‘colorRampPalette’
Mapper: no visible global function definition for ‘terrain.colors’
Mapper: no visible global function definition for ‘points’
Mapper: no visible global function definition for ‘axis’
Standardize: no visible global function definition for ‘lm’
Undefined global functions or variables:
  approx axis colorRampPalette filter lm points terrain.colors
Consider adding
  importFrom("grDevices", "colorRampPalette", "terrain.colors")
  importFrom("graphics", "axis", "points")
  importFrom("stats", "approx", "filter", "lm")
to your NAMESPACE file.
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 ‘plot’
bd.shifts.plot: no visible global function definition for ‘lines’
bdsky.stt.optim: no visible global function definition for ‘optim’
create.mat: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  lines optim optimize plot read.table uniroot write.table
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "optim", "optimize", "uniroot")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
plot.treeperm: no visible global function definition for ‘hist’
plot.treeperm: no visible global function definition for ‘points’
plot.treeperm: no visible global function definition for ‘text’
treeperm.formula: no visible global function definition for
  ‘model.frame’
treeperm.formula: no visible global function definition for
  ‘model.response’
Undefined global functions or variables:
  hist model.frame model.response points text
Consider adding
  importFrom("graphics", "hist", "points", "text")
  importFrom("stats", "model.frame", "model.response")
to your NAMESPACE file.
Running examples in ‘TreeSim-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sim.bd.age
> ### Title: sim.bd.age: Simulating birth-death trees of a fixed age.
> ### Aliases: sim.bd.age
> 
> ### ** Examples
> 
> age<-2
> lambda <- 2.0
> mu <- 0.5
> frac <-0.6
> numbsim<-3
> 
> ##
> # Simulating trees with time age since the origin:
> 
> sim.bd.age(age,numbsim,lambda,mu,mrca=FALSE,complete=TRUE)
[[1]]

Phylogenetic tree with 117 tips and 116 internal nodes.

Tip labels:
	t51, t46, t102, t11, t8, t87, ...

Rooted; includes branch lengths.

[[2]]
[1] 0

[[3]]
[1] 0

> sim.bd.age(age,numbsim,lambda,mu,frac,mrca=FALSE,complete=FALSE)
Warning in max(oldnodes) :
  no non-missing arguments to max; returning -Inf
Error in integer(max(oldnodes)) : vector size cannot be infinite
Calls: sim.bd.age ... drop.extinct -> .drop.tip -> collapse.singles -> integer
Execution halted
cinbag: no visible global function definition for ‘var’
trimTrees: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict var
Consider adding
  importFrom("stats", "predict", "var")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘gtools’ ‘mgcv’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘gtools’ ‘mgcv’ ‘msm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HtoGp: no visible global function definition for ‘odd’
HtoGp: no visible global function definition for ‘even’
plot.pirls.gam: no visible global function definition for ‘par’
plot.pirls.gam: no visible global function definition for ‘plot’
plot.pirls.gam: no visible global function definition for ‘title’
plot.pirls.gam: no visible global function definition for ‘lines’
plot.pirls.gam: no visible global function definition for ‘rug’
plot.pirls.gam: no visible global function definition for ‘mtext’
test.trioGxE: no visible global function definition for ‘write.table’
trioGxE: no visible global function definition for ‘quantile’
trioGxE: no visible global function definition for ‘qtnorm’
trioplot: no visible global function definition for ‘quantile’
trioplot: no visible global function definition for ‘formula’
trioplot: no visible global function definition for ‘gam’
trioplot: no visible global function definition for ‘binomial’
Undefined global functions or variables:
  binomial even formula gam lines mtext odd par plot qtnorm quantile
  rug title write.table
Consider adding
  importFrom("graphics", "lines", "mtext", "par", "plot", "rug", "title")
  importFrom("stats", "binomial", "formula", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
DrawMargin: no visible global function definition for ‘qnorm’
DrawProbability: no visible global function definition for ‘pnorm’
Factor: no visible global function definition for ‘new’
Gaussian: no visible global function definition for ‘new’
LikelihoodFactor: no visible global function definition for ‘new’
Parameters: no visible global function definition for ‘new’
Player: no visible global function definition for ‘new’
PriorFactor: no visible global function definition for ‘new’
SumFactor: no visible global function definition for ‘new’
TruncateFactor: no visible global function definition for ‘new’
Variable: no visible global function definition for ‘new’
Vdraw: no visible global function definition for ‘dnorm’
Vdraw: no visible global function definition for ‘pnorm’
Vwin: no visible global function definition for ‘dnorm’
Vwin: no visible global function definition for ‘pnorm’
Wdraw: no visible global function definition for ‘dnorm’
Wdraw: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm new pnorm qnorm
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dnorm", "pnorm", "qnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
cdens: no visible global function definition for ‘head’
dplot: no visible global function definition for ‘knots’
dplot: no visible global function definition for ‘median’
dplot: no visible global function definition for ‘par’
dplot: no visible global function definition for ‘plot.stepfun’
dplot: no visible global function definition for ‘abline’
edf: no visible global function definition for ‘approxfun’
mctest : rdist: no visible global function definition for ‘runif’
mctest : S: no visible global function definition for ‘optim’
qplot: no visible global function definition for ‘plot’
qplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline approxfun head knots median optim par plot plot.stepfun runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "approxfun", "knots", "median", "optim",
             "plot.stepfun", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
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’
plot.tsdecomp: no visible global function definition for ‘plot’
setupFormula: no visible global function definition for ‘as.formula’
spatialgibbs: no visible global function definition for ‘rnorm’
spatialgibbs: no visible global function definition for ‘rgamma’
spatialgibbs: no visible global function definition for ‘runif’
tsdecomp: no visible global function definition for ‘fft’
Undefined global functions or variables:
  as.formula complete.cases dist fft glm.control mahalanobis par plot
  quantile rgamma rnorm runif terms
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.formula", "complete.cases", "dist", "fft",
             "glm.control", "mahalanobis", "quantile", "rgamma", "rnorm",
             "runif", "terms")
to your NAMESPACE file.
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of ‘penalize.diag’ to
  ‘penalize.diagonal’
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of ‘penalize.diag’ to
  ‘penalize.diagonal’
.help.ESS: no visible global function definition for ‘index.search’
TransSphere : ttin: no visible global function definition for ‘t.test’
TransSphere: no visible global function definition for ‘sd’
TransSphere: no visible global function definition for ‘quantile’
TransSphere: no visible global function definition for ‘pt’
Undefined global functions or variables:
  index.search pt quantile sd t.test
Consider adding
  importFrom("stats", "pt", "quantile", "sd", "t.test")
to your NAMESPACE file.
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.
Found the following significant warnings:
  libqhull/rboxlib.c:351:5: warning: ‘strncat’ output may be truncated copying between 0 and 199 bytes from a string of length 199 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TukeyRegion.Rcheck/00install.out’ for details.
http.connection: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
turf: no visible global function definition for ‘read.table’
turf: no visible global function definition for ‘flush.console’
turf.combos: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn flush.console read.table
Consider adding
  importFrom("utils", "combn", "flush.console", "read.table")
to your NAMESPACE file.
TwoCop: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
txtacf: no visible binding for global variable ‘na.fail’
txtacf: no visible global function definition for ‘acf’
txtboxplot : <anonymous>: no visible global function definition for
  ‘boxplot.stats’
txtboxplot: no visible global function definition for ‘boxplot.stats’
txtdensity: no visible global function definition for ‘density’
Undefined global functions or variables:
  acf boxplot.stats density na.fail
Consider adding
  importFrom("grDevices", "boxplot.stats")
  importFrom("stats", "acf", "density", "na.fail")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/uavRst.Rcheck/00install.out’ for details.
Crm: no visible global function definition for ‘integrate’
Crm : <anonymous>: no visible global function definition for
  ‘integrate’
Crm: no visible global function definition for ‘optimize’
ail1: no visible global function definition for ‘uniroot’
ail2 : fu : <anonymous>: no visible global function definition for
  ‘integrate’
ail2: no visible global function definition for ‘uniroot’
aip : fu : <anonymous>: no visible global function definition for
  ‘integrate’
aip: no visible global function definition for ‘uniroot’
ait1: no visible global function definition for ‘uniroot’
ait2 : fu : <anonymous>: no visible global function definition for
  ‘integrate’
ait2: no visible global function definition for ‘uniroot’
sim3p3: no visible global function definition for ‘rbinom’
simCrm: no visible global function definition for ‘rbinom’
simCrm: no visible global function definition for ‘palette’
simCrm: no visible global function definition for ‘gray’
simCrm: no visible global function definition for ‘plot’
simCrm: no visible global function definition for ‘abline’
simCrm: no visible global function definition for ‘lines’
ssim3p3: no visible global function definition for ‘txtProgressBar’
ssim3p3: no visible global function definition for ‘setTxtProgressBar’
ssimCrm: no visible global function definition for ‘txtProgressBar’
ssimCrm: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  abline gray integrate lines optimize palette plot rbinom
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("grDevices", "gray", "palette")
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "integrate", "optimize", "rbinom", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
rmd2pdf: no visible global function definition for ‘tail’
rnw2pdf: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
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.
src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_CFLAGS without any C files
  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).
Running ‘test_unifDAG.R’ [4s/7s]
Running the tests in ‘tests/test_unifDAG.R’ failed.
Complete output:
  > library(unifDAG)
  > 
  > my.wgtMatrix <- function(g, transpose = TRUE) {
  +   res <- as(g, "matrix") # from 'graph' package, now reliable (we hope)
  +   if (transpose) ## default!
  +     t(res) else res
  + }
  > 
  > ## exact
  > set.seed(123)
  > n <- 2
  > reps <- 100
  > res <- matrix(0, reps, 3)
  > for (i in 1:reps) {
  +     gAM <- unifDAG(n)
  +     wm <- my.wgtMatrix(gAM)
  +     if (wm[1,2] != 0) {
  +         res[i,1] <- 1
  +     } else {
  +           if (wm[2,1] != 0) {
  +               res[i,2] <- 1
  +           } else {
  +                 res[i,3] <- 1
  +             }
  +       }
  + }
  > if (!all(round(colMeans(res), 2) == c(0.41, 0.31, 0.28))) {
  +     stop("test_unifDAG: Saved result could not be reproduced (unifDAG).")
  + }
  Error: test_unifDAG: Saved result could not be reproduced (unifDAG).
  Execution halted
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 ‘testthat.R’ [17s/24s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(utiml)
  Loading required package: mldr
  Loading required package: parallel
  > 
  > test_check("utiml")
  ── 1. Failure: Bipartition measures (@test_evaluation.R#153)  ──────────────────
  mean(utiml_measure_macro_f1(mlconfmat)) not equal to measures$MacroFMeasure.
  1/1 mismatches
  [1] 0.275 - NaN == NaN
  
  ── 2. Failure: iterative kfold (@test_sampling.R#238)  ─────────────────────────
  length(f1$fold[[2]]) not equal to 25.
  1/1 mismatches
  [1] 24 - 25 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1155 SKIPPED: 21 FAILED: 2
  1. Failure: Bipartition measures (@test_evaluation.R#153) 
  2. Failure: iterative kfold (@test_sampling.R#238) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘uuid/libs/uuid.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘gen_uuid.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘gen_uuid.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 significant warnings:
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<> >::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::MemoryPoolAllocator<> >’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<> >’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::CrtAllocator>’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/validatejsonr.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("vanddraabe")
  Loading required package: vanddraabe
  ── 1. Failure: the correct mobility values are returned (@test-BoundWaterEnviron
  Mobility(Bvalues, occupancy) not equal to `mobility.answer`.
  14/14 mismatches (average diff: 0.0382)
  [1] 0.224 - 0.225 == -0.00168
  [2] 0.373 - 0.375 == -0.00280
  [3] 0.471 - 0.474 == -0.00354
  [4] 0.621 - 0.626 == -0.00467
  [5] 0.706 - 0.676 ==  0.03025
  [6] 0.824 - 0.876 == -0.05229
  [7] 0.993 - 0.948 ==  0.04521
  [8] 1.006 - 1.013 == -0.00756
  [9] 1.242 - 1.126 ==  0.11578
  ...
  
  ── 2. Failure: counting AtomTypes works (@test-utilities.R#102)  ───────────────
  getAtomTypeCounts(atom.types) not equal to `ATCounts.answer`.
  56/167 mismatches (average diff: 5.09)
  [4]  0 - 1 == -1
  [9]  0 - 8 == -8
  [11] 0 - 7 == -7
  [14] 7 - 1 ==  6
  [15] 1 - 0 ==  1
  [18] 0 - 1 == -1
  [21] 0 - 1 == -1
  [23] 0 - 4 == -4
  [31] 1 - 0 ==  1
  ...
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 63 SKIPPED: 0 FAILED: 2
  1. Failure: the correct mobility values are returned (@test-BoundWaterEnvironments.R#71) 
  2. Failure: counting AtomTypes works (@test-utilities.R#102) 
  
  Error: testthat unit tests failed
  Execution halted
Mammen: no visible global function definition for ‘runif’
PR2: no visible global function definition for ‘ar.burg’
PR2: no visible global function definition for ‘pt’
PR2: no visible global function definition for ‘pf’
PR3: no visible global function definition for ‘ar.burg’
PR3: no visible global function definition for ‘pt’
PR3: no visible global function definition for ‘pf’
VAR.FOR: no visible global function definition for ‘qnorm’
VAR.ForeB: no visible global function definition for ‘runif’
VAR.LRtest: no visible global function definition for ‘pchisq’
VAR.LRtest: no visible global function definition for ‘pf’
VAR.PI: no visible global function definition for ‘quantile’
VAR.Waldtest: no visible global function definition for ‘pf’
VAR.irf: no visible global function definition for ‘par’
VAR.irf: no visible global function definition for ‘plot’
VAR.irf: no visible global function definition for ‘abline’
VAR1.sim: no visible global function definition for ‘rnorm’
resamp: no visible global function definition for ‘runif’
Undefined global functions or variables:
  abline ar.burg par pchisq pf plot pt qnorm quantile rnorm runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "ar.burg", "pchisq", "pf", "pt", "qnorm",
             "quantile", "rnorm", "runif")
to your NAMESPACE file.
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.
cv.vda.le.default: no visible global function definition for ‘predict’
cv.vda.r.default: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Running examples in ‘VDA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cv.vda.le
> ### Title: Choose the optimal pair of lambdas, lambda_1 and lambda_2
> ### Aliases: cv.vda.le cv.vda.le.default
> 
> ### ** Examples
> 
> ### load zoo data
> ### column 1 is name, columns 2:17 are features, column 18 is class
> data(zoo)
> 
> ### feature matrix 
> x <- zoo[,2:17]
> 
> ### class vector
> y <- zoo[,18]
> 
> ### lambda vector
> lam1 <- (1:5)/100
> lam2 <- (1:5)/100
> 
> ### Searching for the best pair, using both lasso and euclidean penalizations
> cv <- cv.vda.le(x, y, kfold = 3, lam.vec.1 = exp(1:5)/10000, lam.vec.2 = (1:5)/100)
Error in if (sumcoeff[j] != 0) { : missing value where TRUE/FALSE needed
Calls: cv.vda.le -> cv.vda.le.default -> vda.le -> vda.le.default
Execution halted
Compare2FDS: no visible global function definition for ‘runif’
Compare2FDS: no visible global function definition for ‘lm’
Compare2FDS: no visible global function definition for ‘model.matrix’
Compare2FDS: no visible global function definition for ‘plot’
Compare2FDS: no visible global function definition for ‘abline’
Compare2FDS: no visible global function definition for ‘lines’
Compare2FDS: no visible global function definition for ‘text’
Compare2Vdg: no visible global function definition for ‘par’
Compare2Vdg: no visible global function definition for ‘plot’
Compare2Vdg: no visible global function definition for ‘lines’
Compare2Vdg: no visible global function definition for ‘legend’
FDSPlot: no visible global function definition for ‘runif’
FDSPlot: no visible global function definition for ‘lm’
FDSPlot: no visible global function definition for ‘model.matrix’
FDSPlot: no visible global function definition for ‘plot’
FDSPlot: no visible global function definition for ‘abline’
Vdgraph: no visible global function definition for ‘par’
Vdgraph: no visible global function definition for ‘plot’
Vdgraph: no visible global function definition for ‘lines’
Vdgraph: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline legend lines lm model.matrix par plot runif text
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "plot",
             "text")
  importFrom("stats", "lm", "model.matrix", "runif")
to your NAMESPACE file.
calculateParameters,AffineTransformation: no visible global function
  definition for ‘lm’
calculateParameters,AffineTransformation: no visible global function
  definition for ‘coef’
calculateParameters,SimilarityTransformation: no visible global
  function definition for ‘lm’
calculateParameters,SimilarityTransformation: no visible global
  function definition for ‘coef’
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for ‘points’
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for ‘legend’
Undefined global functions or variables:
  coef legend lm points
Consider adding
  importFrom("graphics", "legend", "points")
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
DrawDensity3D: no visible global function definition for ‘colorRamp’
DrawDensity3D: no visible global function definition for ‘rgb’
ReadFromFile3D: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  colorRamp read.table rgb
Consider adding
  importFrom("grDevices", "colorRamp", "rgb")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'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’
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 ‘plot’
Sliding.Window: no visible global function definition for ‘lines’
Sliding.Window: no visible global function definition for ‘legend’
Undefined global functions or variables:
  axis barplot legend lines plot
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "plot")
to your NAMESPACE file.
voss1d: no visible global function definition for ‘approx’
voss1d: no visible global function definition for ‘rnorm’
voss1g: no visible global function definition for ‘dchisq’
voss1g: no visible global function definition for ‘approx’
voss1g: no visible global function definition for ‘rnorm’
voss2d: no visible global function definition for ‘rnorm’
voss2g: no visible global function definition for ‘dchisq’
voss2g: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  approx dchisq rnorm
Consider adding
  importFrom("stats", "approx", "dchisq", "rnorm")
to your NAMESPACE file.
'library' or 'require' call to ‘raster’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
level: no visible global function definition for ‘quantile’
obj.rec: no visible global function definition for ‘txtProgressBar’
obj.rec: no visible global function definition for ‘setTxtProgressBar’
project: no visible global function definition for ‘aggregate’
raster.proj: no visible global function definition for ‘quantile’
raster.proj: no visible global function definition for ‘rasterFromXYZ’
raster.proj: no visible global function definition for ‘plot.new’
raster.proj: no visible global function definition for ‘plot’
raster.proj: no visible global function definition for ‘legend’
sub.obj: no visible global function definition for ‘aggregate’
sub.obj: no visible global function definition for ‘txtProgressBar’
sub.obj: no visible global function definition for ‘setTxtProgressBar’
surface: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  aggregate legend plot plot.new quantile rasterFromXYZ
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "plot", "plot.new")
  importFrom("stats", "aggregate", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'library' or 'require' call to ‘misc3d’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.vscc: no visible global function definition for ‘rainbow’
plot.vscc: no visible global function definition for ‘pairs’
Undefined global functions or variables:
  pairs rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "pairs")
to your NAMESPACE file.
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.
Foreign function call to a different package:
  .C("comwr", ..., PACKAGE = "wavethresh")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
changepoints.sbs: no visible global function definition for ‘mad’
changepoints.wbs: no visible global function definition for ‘var’
changepoints.wbs: no visible global function definition for ‘quantile’
plot.sbs: no visible global function definition for ‘ts.plot’
plot.sbs: no visible global function definition for ‘lines’
plot.sbs: no visible global function definition for ‘title’
random.intervals: no visible global function definition for ‘runif’
sbs.default: no visible global function definition for ‘var’
wbs.default: no visible global function definition for ‘var’
Undefined global functions or variables:
  lines mad quantile runif title ts.plot var
Consider adding
  importFrom("graphics", "lines", "title")
  importFrom("stats", "mad", "quantile", "runif", "ts.plot", "var")
to your NAMESPACE file.
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.
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.
'library' or 'require' call to ‘markdown’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  tabix/razf.c:188:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/WhopGenome.Rcheck/00install.out’ for details.
dlog.norm: no visible global function definition for ‘rnorm’
fun.load.hals.a: no visible global function definition for ‘sfExport’
fun.load.hals.a: no visible global function definition for ‘sfLibrary’
fun.load.hals.fill: no visible global function definition for
  ‘sfExport’
fun.load.hals.fill: no visible global function definition for
  ‘sfLibrary’
fun.load.widals.a: no visible global function definition for ‘sfExport’
fun.load.widals.a: no visible global function definition for
  ‘sfLibrary’
fun.load.widals.fill: no visible global function definition for
  ‘sfExport’
fun.load.widals.fill: no visible global function definition for
  ‘sfLibrary’
unif.mh: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif sfExport sfLibrary
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘genefilter’ ‘parallel’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for
  ‘packageDescription’
.relax.cvcompute: no visible binding for global variable
  ‘weighted.mean’
.relax.widenet.cv.elnet: no visible global function definition for
  ‘predict’
.relax.widenet.cv.elnet: no visible binding for global variable
  ‘weighted.mean’
.relax.widenet.cv.lognet: no visible global function definition for
  ‘predict’
.relax.widenet.cv.lognet: no visible binding for global variable
  ‘weighted.mean’
.widenet.cv.elnet: no visible global function definition for ‘predict’
.widenet.cv.elnet: no visible binding for global variable
  ‘weighted.mean’
.widenet.cv.lognet: no visible global function definition for ‘predict’
.widenet.cv.lognet: no visible binding for global variable
  ‘weighted.mean’
predict.widenet: no visible global function definition for ‘predict’
screen.cor : <anonymous>: no visible global function definition for
  ‘var’
screen.cor : <anonymous>: no visible global function definition for
  ‘cor.test’
screen.ttest: no visible global function definition for ‘colttests’
widenet: no visible global function definition for ‘mc.reset.stream’
widenet: no visible global function definition for ‘mclapply’
widenet: no visible global function definition for ‘predict’
Undefined global functions or variables:
  colttests cor.test mc.reset.stream mclapply packageDescription
  predict var weighted.mean
Consider adding
  importFrom("stats", "cor.test", "predict", "var", "weighted.mean")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
Bundesliga.Mannschaft: no visible global function definition for ‘data’
Bundesliga.Mannschaft: no visible binding for global variable
  ‘Bundesliga’
Bundesliga.Tabelle: no visible global function definition for ‘data’
Bundesliga.Tabelle: no visible binding for global variable ‘Bundesliga’
Bundesliga.XML: no visible global function definition for ‘data’
Bundesliga.XML: no visible binding for global variable ‘Bundesliga’
sens.spec: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.

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’.
Error(s) in re-building vignettes:
  ...
--- re-building ‘wikisourcer.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

Quitting from lines 78-81 (wikisourcer.Rmd) 
Error: processing vignette 'wikisourcer.Rmd' failed with diagnostics:
HTTP error 404.
--- failed re-building ‘wikisourcer.Rmd’

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

Error: Vignette re-building failed.
Execution halted
wilcox.selection.split: no visible global function definition for
  ‘pnorm’
wilcox.test2: no visible global function definition for ‘wilcox.test’
Undefined global functions or variables:
  pnorm wilcox.test
Consider adding
  importFrom("stats", "pnorm", "wilcox.test")
to your NAMESPACE file.
Cs: no visible global function definition for ‘wilcox.test’
Don: no visible global function definition for ‘points’
Don: no visible global function definition for ‘chisq.test’
Lixn: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  chisq.test pchisq points wilcox.test
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "chisq.test", "pchisq", "wilcox.test")
to your NAMESPACE file.
plotTrait: no visible global function definition for ‘plot’
plotTrait: no visible global function definition for ‘points’
plotTrait: no visible global function definition for ‘legend’
test.windex: no visible global function definition for ‘hist’
test.windex: no visible global function definition for ‘abline’
test.windex: no visible global function definition for ‘legend’
windex: no visible global function definition for ‘sd’
windex: no visible global function definition for ‘var’
windex: no visible global function definition for ‘dist’
windex: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline dist hist legend plot points quantile sd var
Consider adding
  importFrom("graphics", "abline", "hist", "legend", "plot", "points")
  importFrom("stats", "dist", "quantile", "sd", "var")
to your NAMESPACE file.
dbayes: no visible global function definition for ‘mahalanobis’
dbayes: no visible global function definition for ‘var’
wmd: no visible global function definition for ‘cor’
wmd: no visible global function definition for ‘var’
Undefined global functions or variables:
  cor mahalanobis var
Consider adding
  importFrom("stats", "cor", "mahalanobis", "var")
to your NAMESPACE file.
fit,Leader: no visible global function definition for ‘lm’
plotfit,Leader: no visible global function definition for ‘par’
plotfit,Leader: no visible global function definition for ‘plot’
Undefined global functions or variables:
  lm par plot
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
Running ‘testthat.R’ [3s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(WMWssp)
  > 
  > test_check("WMWssp")
  Simulation:
  
  Wilcoxon-Mann-Whitney Sample Size Calculation
   
  Summary
  Call: eval
  Type-I error (two-sided): 0.05
  Power: 0.8
  
                                   Results
  alpha (2-sided)                0.0500000
  Power                          0.8000000
  Simulated Power                0.7600000
  N (total sample size needed)   0.3491124
  t=n1/N                       111.3664650
  n1 in Group 1                  0.4964905
  n2 in Group 2                 55.2923889
  N rounded for t = 1/2         56.0740762
  N rounded                    112.0000000
  n1 rounded                   113.0000000
  n2 rounded                    56.0000000
  12                            57.0000000
  ── 1. Failure: function WMWssp_minimize (@test_MinMax.R#22)  ───────────────────
  `result_power` not equivalent to `result_simpower`.
  1/1 mismatches
  [1] 0.92 - 0.76 == 0.16
  
  Simulation:
  
  ── 2. Failure: function WMWssp (@test_WMWssp.R#21)  ────────────────────────────
  `result_power` not equivalent to `result_simpower`.
  1/1 mismatches
  [1] 0.9 - 0.7 == 0.2
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 14 SKIPPED: 0 FAILED: 2
  1. Failure: function WMWssp_minimize (@test_MinMax.R#22) 
  2. Failure: function WMWssp (@test_WMWssp.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
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
src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_CFLAGS without any C files
  src/Makevars: incorrect macro SHLIB_OPENMP_CFLAGS included in PKG_CXXFLAGS
  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).
simul.wsvm: no visible binding for global variable ‘mixture.example’
wsvm.boost: no visible global function definition for ‘plot’
Undefined global functions or variables:
  mixture.example plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
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’ [54s/59s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(xgboost)
  > 
  > test_check("xgboost")
  [1]	train-error:0.061262 
  ── 1. Failure: xgb.cv works (@test_basic.R#185)  ───────────────────────────────
  cv$evaluation_log[, min(test_error_std)] is not strictly less than 0.004. Difference: 0.00328
  
  [1]	train-logloss:0.380601 
  [2]	train-logloss:0.247327 
  [3]	train-logloss:0.175046 
  [4]	train-logloss:0.122303 
  [5]	train-logloss:0.089890 
  [1]	train-logloss:0.497351 
  [2]	train-logloss:0.357289 
  [3]	train-logloss:0.257217 
  [4]	train-logloss:0.184524 
  [5]	train-logloss:0.132112 
  [1]	train-auc:0.900000	test-auc:0.800000 
  ── 2. Failure: prediction in early-stopping xgb.cv works (@test_callbacks.R#301)
  abs(err_pred - err_log_last) is not strictly more than 1e-04. Difference: -9.99e-05
  
  [1]	eval-error:0.042831	train-error:0.046522 
  [2]	eval-error:0.021726	train-error:0.022263 
  [1]	eval-error:0.042831	train-error:0.046522 
  [2]	eval-error:0.021726	train-error:0.022263 
  [1]	train-error:0.046522 
  [2]	train-error:0.022263 
  [1]	train-error:0.333333 
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 562 SKIPPED: 4 FAILED: 2
  1. Failure: xgb.cv works (@test_basic.R#185) 
  2. Failure: prediction in early-stopping xgb.cv works (@test_callbacks.R#301) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Package suggested but not available for checking: ‘ggbio’
XHWE: no visible global function definition for ‘read.table’
result: no visible global function definition for ‘pchisq’
result: no visible global function definition for ‘rbinom’
result: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  pchisq rbinom read.table rmultinom
Consider adding
  importFrom("stats", "pchisq", "rbinom", "rmultinom")
  importFrom("utils", "read.table")
to your NAMESPACE file.
R5.value.default: no visible binding for global variable ‘data.table’
R5.value.default: no visible global function definition for
  ‘as.data.table’
R5.value.parse: no visible binding for global variable ‘data.table’
R5.value.parse: no visible global function definition for
  ‘is.data.table’
R5.value.parse: no visible global function definition for
  ‘as.data.table’
stampme: no visible global function definition for ‘flush.console’
stampmsg: no visible global function definition for ‘flush.console’
write.data.table: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  as.data.table data.table flush.console is.data.table write.table
Consider adding
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
File ‘xml2/libs/xml2.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_WriteConnection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard files/directories found at top level:
  ‘Bug.R’ ‘Bugs.html’ ‘Check’ ‘CodeDetails’ ‘DESCRIPTION.in’ ‘Docs’
  ‘FAQ.html’ ‘FIXME_NOW’ ‘GNUmakefile’ ‘GNUmakefile.admin’
  ‘Makevars.in’ ‘MemoryBug.R’ ‘NAMESPACE.in’ ‘NodeFuns’ ‘Notes’
  ‘QuestionSolutions’ ‘README.windows’ ‘Rsamples’ ‘TAGS’
  ‘Todo-orig.html’ ‘Todo.xml’ ‘VersionInfo’ ‘addFinalizer’ ‘checkLinks’
  ‘dotCalls’ ‘expat’ ‘index.html’ ‘index.html.in’ ‘libxml’
  ‘libxml2.9.R’ ‘scrapingData.xml’ ‘testRemoveFinalizers.R’
  ‘testRemoveFinalizers.c’ ‘xpathPointer.xml’
newXMLDoc: no visible binding for global variable ‘doc’
source: no visible binding for global variable ‘use_file’
xmlFlatListTree : f: no visible binding for global variable ‘nodeNames’
xmlFlatListTree : f: no visible binding for global variable ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘nodeSet’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘nodeSet’
xmlFlatListTree : addNode: no visible binding for global variable ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘nodeNames’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘nodeNames’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘parentCount’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘parentCount’
xmlFlatListTree : <anonymous>: no visible binding for global variable
  ‘e’
xmlFlatTree : <anonymous>: no visible binding for global variable ‘e’
Undefined global functions or variables:
  doc e idx nodeNames nodeSet parentCount use_file
LPGM: no visible global function definition for ‘flush.console’
PGM: no visible global function definition for ‘flush.console’
PGM.path.neighborhood: no visible global function definition for
  ‘runif’
PGMSim: no visible global function definition for ‘rpois’
PGMSim: no visible global function definition for ‘par’
WPGMSim: no visible global function definition for ‘rpois’
XMRF.Sim: no visible global function definition for ‘cov2cor’
XMRF.Sim: no visible global function definition for ‘rbinom’
XMRF.Sim: no visible global function definition for ‘rnorm’
glm.generic: no visible global function definition for ‘flush.console’
mymult: no visible global function definition for ‘rmultinom’
plot.GMS: no visible global function definition for ‘pdf’
plot.GMS: no visible global function definition for ‘dev.off’
plotNet: no visible global function definition for ‘pdf’
plotNet: no visible global function definition for ‘dev.off’
print.GMS: no visible global function definition for ‘str’
processSeq: no visible binding for global variable ‘quantile’
processSeq: no visible binding for global variable ‘var’
processSeq: no visible global function definition for ‘ks.test’
rmpois : <anonymous>: no visible global function definition for ‘rpois’
Undefined global functions or variables:
  cov2cor dev.off flush.console ks.test par pdf quantile rbinom
  rmultinom rnorm rpois runif str var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "cov2cor", "ks.test", "quantile", "rbinom",
             "rmultinom", "rnorm", "rpois", "runif", "var")
  importFrom("utils", "flush.console", "str")
to your NAMESPACE file.
File which contains pragma(s) suppressing diagnostics:
  ‘inst/include/xtensor/xstorage.hpp’
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.
bootstrapswapcurve: no visible global function definition for ‘ts’
fitted: no visible global function definition for ‘ts’
forwardrates: no visible global function definition for ‘ts’
residuals: no visible global function definition for ‘ts’
tZC_NS: no visible global function definition for ‘cmpfun’
tZC_NS_extra: no visible global function definition for ‘cmpfun’
tZC_SV: no visible global function definition for ‘cmpfun’
tZC_SV_extra: no visible global function definition for ‘cmpfun’
ycextra: no visible global function definition for ‘new’
ycinter: no visible global function definition for ‘new’
ycplot: no visible global function definition for ‘par’
ycplot: no visible global function definition for ‘points’
ycplot: no visible global function definition for ‘abline’
ycplot: no visible global function definition for ‘hist’
ycplot: no visible global function definition for ‘lines’
ycplot: no visible global function definition for ‘density’
ycplot: no visible global function definition for ‘qqnorm’
ycplot: no visible global function definition for ‘qqline’
ycsummary: no visible global function definition for ‘shapiro.test’
ycsummary: no visible global function definition for ‘pf’
Undefined global functions or variables:
  abline cmpfun density hist lines new par pf points qqline qqnorm
  shapiro.test ts
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "par", "points")
  importFrom("methods", "new")
  importFrom("stats", "density", "pf", "qqline", "qqnorm",
             "shapiro.test", "ts")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.NS.estimator: no visible global function definition for ‘lm’
.NS.estimator: no visible global function definition for ‘coef’
.NS.estimator: no visible global function definition for ‘na.omit’
.NS.estimator: no visible global function definition for ‘resid’
.NSS.estimator: no visible global function definition for ‘lm’
.NSS.estimator: no visible global function definition for ‘coef’
.NSS.estimator: no visible global function definition for ‘na.omit’
.NSS.estimator: no visible global function definition for ‘resid’
NSrates: no visible global function definition for ‘time’
Nelson.Siegel: no visible global function definition for ‘optimize’
Srates: no visible global function definition for ‘time’
Svensson: no visible global function definition for ‘median’
Svensson: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  coef lm median na.omit optimize resid time
Consider adding
  importFrom("stats", "coef", "lm", "median", "na.omit", "optimize",
             "resid", "time")
to your NAMESPACE file.
kmeansN: no visible global function definition for ‘kmeans’
kmeansN: no visible global function definition for ‘aggregate’
kmeansN2: no visible global function definition for ‘aggregate’
kmeansN2: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  aggregate kmeans sd
Consider adding
  importFrom("stats", "aggregate", "kmeans", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: ‘zdat’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/zonator.Rcheck/00install.out’ for details.
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:
  ‘httr’ ‘progress’
  All declared Imports should be used.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    bootstrapping_example   1.2Mb
    libs                    6.2Mb
src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
  src/Makevars.in: 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).
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  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
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 13.8Mb
  sub-directories of 1Mb or more:
    R  13.7Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
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)
File ‘adaptivetau/libs/adaptivetau.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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: ‘filehash’
  All declared Imports should be used.
Running examples in ‘adehabitatMA-Ex.R’ failed
The error most likely occurred in:

> ### Name: buffer
> ### Title: Compute Buffers Regions
> ### Aliases: buffer
> ### Keywords: spatial
> 
> ### ** Examples
> 
> 
> data(lynxjura)
> 
> # locs is the SpatialPointsDataFrame containing the
> # locations of lynx indices in the Jura mountains
> locs <- lynxjura$locs
> head(locs)
        coordinates     Date Type
3 (856208, 2135450) 19801231   EP
4 (852942, 2134370) 19810101   EP
5 (857408, 2134780) 19810101    E
7 (857425, 2135190) 19810114    E
8 (853543, 2133730) 19810114    E
9 (852771, 2132560) 19810114    E
Coordinate Reference System (CRS) arguments: NA 
> 
> ## just for the sake of illustration: sample 100 points
> set.seed(233)
> locs <- locs[sample(1:nrow(locs), 100),]
> 
> # sa is the SpatialPixelsDataFrame object containing
> # maps of the study area
> sa <- lynxjura$map
> 
> # Buffer of 2000 m from all points
> bu <- buffer(locs, sa, 2000)
> image(bu)
> 
> # displays all the pixels of the study area within 2000 m
> # of a point, for each type of indices (see ?lynxjura)
> buani <- buffer(locs[,2], sa, 2000)
> buani
Object of class "SpatialPixelsDataFrame" (package sp):

Grid parameters:
  cellcentre.offset cellsize cells.dim
x            828916      500        96
y           2130700      500        90

Variables measured:
  D E EF EO EP L O OP P
1 0 0  0  0  0 0 0  0 0
2 0 0  0  0  0 0 0  0 0
3 0 0  0  0  0 0 0  0 0
4 0 0  0  0  0 0 0  0 0
5 0 0  0  0  0 0 0  0 0
6 0 0  0  0  0 0 0  0 0
...

> par(mar=c(0,0,2,0))
> opar<-par(mfrow=c(3,4))
> lapply(1:11, function(i) {
+    image(buani, i)
+    title(main = names(slot(buani, "data"))[i])
+ })
Error in `[.data.frame`(x@data, , i, drop = FALSE) : 
  undefined columns selected
Calls: lapply ... matrix -> t -> matrix -> [ -> [ -> [ -> [.data.frame
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.2Mb
File ‘adimpro/libs/adimpro.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘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.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
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  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘devtools’ ‘httpuv’ ‘imager’ ‘purrr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reshape2’
  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.
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.
Namespace in Imports field not imported from: ‘htmlwidgets’
  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.
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.
Namespaces in Imports field not imported from:
  ‘rjson’ ‘xml2’
  All declared Imports should be used.
File ‘algstat/libs/algstat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
Namespaces in Imports field not imported from:
  ‘base’ ‘methods’ ‘nlme’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
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.
File ‘AMORE/libs/AMORE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘magrittr’
  All declared Imports should be used.
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    libs  25.9Mb
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.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rgdal’
  All declared Imports should be used.
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs  23.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    help   4.7Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(anonymizer)
  > 
  > test_check("anonymizer")
  ── 1. Failure: Produces the correct output. (@test-anonymize.R#5)  ─────────────
  anonymize("a", .seed = 1) not equal to "ed879445e47969394b3f8eb818501976bed22b9ab0e7f7c5fdf2a96df0aec80e".
  1/1 mismatches
  x[1]: "6ae80dd07643618a5ea6ac83b506fd367d81f86e5f5650a42045ca7ebe516602"
  y[1]: "ed879445e47969394b3f8eb818501976bed22b9ab0e7f7c5fdf2a96df0aec80e"
  
  ── 2. Failure: Produces the correct output. (@test-salt.R#6)  ──────────────────
  salt("a", .seed = 1, .n_chars = 1) not equal to "gag".
  1/1 mismatches
  x[1]: "yay"
  y[1]: "gag"
  
  ── 3. Failure: Produces the correct output. (@test-salt.R#7)  ──────────────────
  salt("a", .seed = 2, .n_chars = 1) not equal to "eae".
  1/1 mismatches
  x[1]: "uau"
  y[1]: "eae"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 12 SKIPPED: 1 FAILED: 3
  1. Failure: Produces the correct output. (@test-anonymize.R#5) 
  2. Failure: Produces the correct output. (@test-salt.R#6) 
  3. Failure: Produces the correct output. (@test-salt.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
Running examples in ‘Anthropometry-Ex.R’ failed
The error most likely occurred in:

> ### Name: projShapes
> ### Title: Helper function for plotting the shapes
> ### Aliases: projShapes
> ### Keywords: math
> 
> ### ** Examples
> 
> landmarksNoNa <- na.exclude(landmarksSampleSpaSurv)
> dim(landmarksNoNa) 
[1] 574 198
> #[1] 574 198 
> numLandmarks <- (dim(landmarksNoNa)[2]) / 3
> #[1] 66
> #As a toy example, only the first 15 individuals are used.
> landmarksNoNa_First10 <- landmarksNoNa[1:10, ] 
> (numIndiv <- dim(landmarksNoNa_First10)[1])
[1] 10
> #[1] 10         
>     
> array3D <- array3Dlandm(numLandmarks, numIndiv, landmarksNoNa_First10)
> #shapes::plotshapes(array3D[,,1]) 
> #calibrate::textxy(array3D[,1,1], array3D[,2,1], labs = 1:numLandmarks, cex = 0.7) 
> 
> numClust <- 2 ; algSteps <- 1 ; niter <- 1 ; stopCr <- 0.0001
> resLL <- LloydShapes(array3D, numClust, algSteps, niter, stopCr, FALSE, FALSE)
> clust_kmeansProc <- resLL$asig
> 
> prototypes <- anthrCases(resLL)
> 
> projShapes(1, array3D, clust_kmeansProc, prototypes)
Error in if (d2 == 0L) { : missing value where TRUE/FALSE needed
Calls: projShapes -> <Anonymous> -> procrustesGPA -> cnt3 -> apply
Execution halted
Namespaces in Imports field not imported from:
  ‘curl’ ‘httr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
Running ‘testthat.R’ [22s/61s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(aphid)
  > 
  > test_check("aphid")
  ── 1. Failure: Character and raw inputs give same output (@test_PHMM.R#137)  ───
  round(x.vit$score) not equal to round(xDNA.vit$score).
  1/1 mismatches
  [1] 90 - 91 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 44 SKIPPED: 0 FAILED: 1
  1. Failure: Character and raw inputs give same output (@test_PHMM.R#137) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
File ‘appell/libs/appell.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

> ### Name: simplexplot
> ### Title: Simplex visualization
> ### Aliases: simplexplot
> 
> ### ** Examples
> 
> ### This example reproduces parts of the Figure 7 shown in
>   ### "Probabilistic Archetypal Analysis" by Seth and Eugster (2014)
> 
>   data("toy", package = "archetypes")
> 
>   set.seed(1234); a3 <- archetypes(toy, k = 3)
>   set.seed(1237); a4 <- archetypes(toy, k = 4)
>   set.seed(1238); a5 <- archetypes(toy, k = 5)
Warning in archetypes(toy, k = 5) :
  k=5: Error in qr.solve(alphas %*% t(alphas)): singular matrix 'a' in solve

> 
>   simplexplot(a3)
>   simplexplot(a3, show_direction = TRUE, show_points = FALSE)
>   simplexplot(a4, projection = tspsimplex_projection)
Loading required package: TSP
>   simplexplot(a5, show_direction = TRUE, show_points = FALSE,
+     direction_length = 2, directions_col = "black")
Error in rep(points_col, nrow(coef(object))) : invalid 'times' argument
Calls: simplexplot
Execution halted
Namespaces in Imports field not imported from:
  ‘lwgeom’ ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘purrr’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
File ‘arf3DS4/libs/arf3DS4.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘sp’
  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.
File ‘arrApply/libs/arrApply.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.2Mb
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.
File ‘assist/libs/assist.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Running ‘testthat.R’ [28s/40s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(atlantistools)
  > 
  > test_check("atlantistools")
  ── 1. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase
  dim(df1) not equal to c(4, 16).
  1/2 mismatches
  [1] 5 - 4 == 1
  
  ── 2. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase
  df1$linf[3] not equivalent to 87.4.
  1/1 mismatches
  [1] 75.1 - 87.4 == -12.3
  
  ── 3. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase
  df1$k[2] not equivalent to 0.15.
  1/1 mismatches
  [1] 0.53 - 0.15 == 0.38
  
  ── 4. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase
  df1$locality[1] not equivalent to "Central Adriatic, 100-200 m depth".
  1/1 mismatches
  x[1]: "northeast Mediterranean Sea"
  y[1]: "Central Adriatic, 100-200 m depth"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 193 SKIPPED: 1 FAILED: 4
  1. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase.R#6) 
  2. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase.R#7) 
  3. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase.R#8) 
  4. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
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.
File ‘attrCUSUM/libs/attrCUSUM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   9.6Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Output from running autoconf:
  configure.ac:30: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
  ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
  ../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from...
  ../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from...
  configure.ac:30: the top level
  configure.ac:30: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
  ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
  ../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from...
  ../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from...
  ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
  ../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from...
  ../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from...
  configure.ac:30: the top level
  configure.ac:73: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
  ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
  ../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from...
  ../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from...
  ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
  ../../lib/autoconf/libs.m4:47: AC_SEARCH_LIBS is expanded from...
  ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from...
  ../../lib/autoconf/headers.m4:129: _AC_CHECK_HEADER_MONGREL is expanded from...
  ../../lib/autoconf/headers.m4:67: AC_CHECK_HEADER is expanded from...
  ../../lib/m4sugar/m4sh.m4:607: AS_FOR is expanded from...
  ../../lib/autoconf/headers.m4:249: AC_CHECK_HEADERS is expanded from...
  configure.ac:73: the top level
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 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘jsonlite’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.4Mb
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.
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  8.0Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   3.0Mb
Namespace in Imports field not imported from: ‘glpkAPI’
  All declared Imports should be used.
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.
File ‘BAMMtools/libs/BAMMtools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Namespace in Imports field not imported from: ‘zoo’
  All declared Imports should be used.
installed size is 111.9Mb
  sub-directories of 1Mb or more:
    libs  111.1Mb
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ranger’
  All declared Imports should be used.
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  6.2Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.9Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
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.
File ‘BayClone2/libs/BayClone2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘msm’ ‘parallel’ ‘tidyr’
  All declared Imports should be used.
Running ‘testthat.R’ [8s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("bayesCT")
  Loading required package: bayesCT
  
  Attaching package: 'bayesCT'
  
  The following object is masked from 'package:stats':
  
      simulate
  
  ── 1. Failure: The randomization is (@test_randomization.R#8)  ─────────────────
  sum(randomization(12, 10, c(3, 2)) == 1) not equal to 5.
  1/1 mismatches
  [1] 4 - 5 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 41 SKIPPED: 0 FAILED: 1
  1. Failure: The randomization is (@test_randomization.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘bayesDccGarch/libs/bayesDccGarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 72.0Mb
  sub-directories of 1Mb or more:
    libs  71.2Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MatrixModels’
  All declared Imports should be used.
installed size is 23.2Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  16.7Mb
File ‘bayesGARCH/libs/bayesGARCH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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  6.1Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   3.8Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
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  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 31.2Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  26.4Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   4.0Mb
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.
File ‘BayesSingleSub/libs/BayesSingleSub.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  6.1Mb
  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.
installed size is 97.5Mb
  sub-directories of 1Mb or more:
    libs  97.4Mb
File ‘BayHap/libs/BayHap.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘mcmc.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘mcmc.o’
File ‘BayHap/libs/BayHap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor 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:
  ‘ggfortify’ ‘ggplot2’ ‘matrixStats’ ‘reshape2’ ‘scales’
  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.
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 ‘bclust/libs/bclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘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  6.4Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   3.5Mb
Error(s) in re-building vignettes:
--- re-building ‘bdlp.Rmd’ using rmarkdown
Loading required namespace: RSQLite
Warning: call dbDisconnect() when finished working with a connection
Quitting from lines 197-211 (bdlp.Rmd) 
Error: processing vignette 'bdlp.Rmd' failed with diagnostics:
miller2012.R:7:208: unexpected '{'
6:  
7: miller2012 <- function(setnr = NULL, seedinfo = list(100, "3.6.0", c("Mersenne-Twister", "Inversion", "Rejection", metaseedinfo = list(100, "3.6.0", c("Mersenne-Twister", "Inversion", "Rejecti
                                                                                                                                                                                                                  ^
--- failed re-building ‘bdlp.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 108.7Mb
  sub-directories of 1Mb or more:
    libs  107.2Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘chron’ ‘colorspace’ ‘gtable’ ‘htmltools’ ‘htmlwidgets’
  ‘httpuv’ ‘magrittr’ ‘munsell’ ‘plyr’ ‘scales’ ‘stringi’ ‘xtable’
  ‘yaml’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crochet’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘methods’
  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.
Error(s) in re-building vignettes:
--- re-building ‘benthos.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

Quitting from lines 513-514 (benthos.Rmd) 
Error: processing vignette 'benthos.Rmd' failed with diagnostics:
'n' (=100) should be less than the total abundance (=48)
--- failed re-building ‘benthos.Rmd’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 50.4Mb
  sub-directories of 1Mb or more:
    libs  49.4Mb
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.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
File ‘bfa/libs/bfa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 153.5Mb
  sub-directories of 1Mb or more:
    include  153.4Mb
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.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.2Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   6.4Mb
File ‘bigalgebra/libs/bigalgebra.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  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.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
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  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
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  7.6Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   2.5Mb
    libs      1.9Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Running examples in ‘BiG-Ex.R’ failed
The error most likely occurred in:

> ### Name: BiG_DA
> ### Title: BiG with half-t prior through a data augmentation approach
> ### Aliases: BiG_DA
> 
> ### ** Examples
> 
> set.seed(1234)
> sim = sim_lvm(G=25, S=6, n_p1=3, rho=runif(6,min=0.3,max=0.9), p_p1=0.6, p_p2=0.8, 
+       lambda=runif(6,min=0.6,max=0.8), n_T=sample(c(5,10,15),6,replace=TRUE))
> BiG_DA(r=sim$r, n_T=sim$n_T, n_p1=3, M=100, burnin=50)
Warning in max(W[which(r[, s] == (n_T[s] + 1)), s]) :
  no non-missing arguments to max; returning -Inf
Error in truncnorm::rtruncnorm(sum(r[, s] == n_T[s] + 1, na.rm = TRUE),  : 
  length(mean) > 0 is not TRUE
Calls: BiG_DA -> <Anonymous> -> stopifnot
Execution halted
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 11.6Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      8.8Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
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 17.5Mb
  sub-directories of 1Mb or more:
    libs  16.9Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   9.0Mb
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.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
File ‘Binarize/libs/Binarize.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   2.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Package suggested but not available for checking: ‘BiocVersion’
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   8.7Mb
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  6.2Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Running examples in ‘bipartite-Ex.R’ failed
The error most likely occurred in:

> ### Name: genweb
> ### Title: Generate a random bipartite web
> ### Aliases: genweb
> ### Keywords: package
> 
> ### ** Examples
> 
> genweb()

Execution halted
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.
File ‘bit/libs/bit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘corrgram’ ‘rpivotTable’ ‘shinyAce’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Package suggested but not available for checking: ‘RQuantLib’
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
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  7.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   3.1Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’
  ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
Missing or unexported object: ‘xgboost::predict’
installed size is 54.7Mb
  sub-directories of 1Mb or more:
    libs  53.4Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Running ‘testthat.R’ [28s/74s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(blockForest)
  > 
  > test_check("blockForest")
  ── 1. Failure: standard error is larger for fewer trees, probability (@test_jack
  mean(pred50$se) is not strictly less than mean(pred5$se). Difference: 0.0317
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 415 SKIPPED: 0 FAILED: 1
  1. Failure: standard error is larger for fewer trees, probability (@test_jackknife.R#159) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘blockingChallenge-Ex.R’ failed
The error most likely occurred in:

> ### Name: makeblocks
> ### Title: Creates strata of size 'bsize' aiming to minimize within strata
> ###   distance.
> ### Aliases: makeblocks
> ### Keywords: Challenge Stratification algorithm
> 
> ### ** Examples
> 
> ## IN THESE EXAMPLES YOU NEED TO LOAD THE R PACKAGE 
> #  'optmatch'.  OTHERWISE, THEY WILL RUN IN A CODE CHECK MODE.
> # library(optmatch)
> ###### 		Usage 1		##########
> data(nh0506)
> ## Don't show: 
> 	nh0506 <- nh0506[1:13,]
> ## End(Don't show)
> res <- makeblocks(nh0506, bsize=4, maxItr=15, 
+          vars=c("female","age","black","hispanic","education","povertyr"))
Iteration no. 1 :: Error in pairmatch(distmat.temp1, controls = bsize - 1) : 
  could not find function "pairmatch"
Calls: makeblocks -> eval -> eval
Execution halted
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
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.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
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:
  ‘formula.tools’ ‘plm’
  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 35.1Mb
  sub-directories of 1Mb or more:
    libs  34.8Mb
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 69.9Mb
  sub-directories of 1Mb or more:
    libs  69.6Mb
Running ‘testthat.R’ [244s/569s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BMSC)
  Loading required package: Rcpp
  > 
  > test_check("BMSC")
  ── 1. Failure: A message is returned if some rows are missing (@test_missingValu
  `BMSC:::handleMissingData(data, formula, yUncertainty)$data` produced unexpected messages.
  Expected match: 7 rows \\(9.33% of the data\\) were excluded due to missing values.
  Actual values:
  * 8 rows (10.67% of the data) were excluded due to missing values.
  
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 61 SKIPPED: 1 FAILED: 1
  1. Failure: A message is returned if some rows are missing (@test_missingValuesHandling.R#47) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [3m/80m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BMTME)
  > 
  > test_check("BMTME")
  	2 slaves are spawned successfully. 0 failed.
  [warn] Epoll ADD(4) on fd 38 failed.  Old events were 0; read change was 0 (none); write change was 1 (add): Bad file descriptor
  [warn] Epoll ADD(4) on fd 0 failed.  Old events were 0; read change was 0 (none); write change was 1 (add): Bad file descriptor
  	2 slaves are spawned successfully. 0 failed.
  --------------------------------------------------------------------------
  (null) noticed that process rank 1 with PID 0 on node gannet exited on signal 15 (Terminated).
  --------------------------------------------------------------------------
Error(s) in re-building vignettes:
--- re-building ‘bme.Rmd’ using rmarkdown
--- finished re-building ‘bme.Rmd’

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

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

--- re-building ‘bmtme.Rmd’ using rmarkdown
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.7Mb
installed size is 402.5Mb
  sub-directories of 1Mb or more:
    include    3.2Mb
    lib      399.0Mb
installed size is 89.2Mb
  sub-directories of 1Mb or more:
    libs  88.8Mb
Namespace in Imports field not imported from: ‘psych’
  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.
File ‘bootstrap/libs/bootstrap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
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.
installed size is 41.3Mb
  sub-directories of 1Mb or more:
    libs  41.1Mb
Namespace in Imports field not imported from: ‘lme4’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘profileModel’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R     2.9Mb
    doc   1.8Mb
Running ‘testthat.R’ [4m/12m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(brms)
  Loading required package: Rcpp
  Loading required package: ggplot2
  Loading 'brms' package (version 2.7.0). Useful instructions
  can be found by typing help('brms'). A more detailed introduction
  to the package is available through vignette('brms_overview').
  Run theme_set(theme_default()) to use the default bayesplot theme.
  > 
  > test_check("brms")
  ── 1. Failure: first_greater returns expected results (@tests.brmsfit-helpers.R#
  first_greater(A, x) not equal to c(3, 3, 3, 3, 2, 1, 2, 2, 2, 3).
  4/10 mismatches (average diff: 1.5)
  [6]  3 - 1 ==  2
  [7]  1 - 2 == -1
  [8]  3 - 2 ==  1
  [10] 1 - 3 == -2
  
  ── 2. Failure: first_greater returns expected results (@tests.brmsfit-helpers.R#
  first_greater(A, x, i = 2) not equal to c(3, 3, 3, 3, 2, 2, 2, 2, 2, 3).
  3/10 mismatches (average diff: 1)
  [6]  3 - 2 ==  1
  [8]  3 - 2 ==  1
  [10] 2 - 3 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1263 SKIPPED: 4 FAILED: 2
  1. Failure: first_greater returns expected results (@tests.brmsfit-helpers.R#7) 
  2. Failure: first_greater returns expected results (@tests.brmsfit-helpers.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    bin    2.5Mb
    doc    1.1Mb
    libs   2.5Mb
Namespaces in Imports field not imported from:
  ‘rworldxtra’ ‘sp’
  All declared Imports should be used.
Found the following significant warnings:
  helpers.c:365:19: warning: absolute value function 'fabsf' given an argument of type 'double' but has parameter of type 'float' which may cause truncation of value [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/BSquare.Rcheck/00install.out’ for details.
File ‘BSquare/libs/BSquare.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    libs  33.2Mb
installed size is 104.4Mb
  sub-directories of 1Mb or more:
    libs  103.8Mb
File ‘BTR/libs/BTR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
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.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
File ‘Cairo/libs/Cairo.so’:
  Found non-API calls to R: ‘R_InputHandlers’, ‘addInputHandler’
File ‘Cairo/libs/Cairo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R        1.1Mb
    data     1.6Mb
    models   2.4Mb
Running ‘testthat.R’ [114s/280s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(caret)
  Loading required package: lattice
  Loading required package: ggplot2
  > 
  > test_check("caret")
  OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
  OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  ── 1. Failure: twoClassSummary is calculating correctly (@test_twoClassSummary.R
  mod1$resample$ROC not equal to mod2$resample$ROC.
  2/25 mismatches (average diff: 0.0045)
  [18] 0.836 - 0.831 ==  0.00529
  [21] 0.537 - 0.541 == -0.00370
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 105 SKIPPED: 32 FAILED: 1
  1. Failure: twoClassSummary is calculating correctly (@test_twoClassSummary.R#31) 
  
  Error: testthat unit tests failed
  Execution halted
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.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   3.4Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘cowplot’ ‘dplyr’ ‘ranger’ ‘rms’ ‘survival’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
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.
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 ‘caTools/libs/caTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      1.2Mb
    extdata   1.1Mb
    libs      2.7Mb
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.
File ‘ccaPP/libs/ccaPP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
estim.regul: warning in matrix(res, nc = length(grid2)): partial
  argument match of 'nc' to 'ncol'
comput: no visible global function definition for ‘cor’
img.estim.regul: no visible global function definition for ‘par’
img.estim.regul: no visible global function definition for ‘image’
img.estim.regul: no visible global function definition for
  ‘heat.colors’
img.estim.regul: no visible global function definition for ‘axis’
img.estim.regul: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘par’
img.matcor: no visible global function definition for ‘image’
img.matcor: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘abline’
img.matcor: no visible global function definition for ‘layout’
loo: no visible global function definition for ‘cor’
matcor: no visible global function definition for ‘cor’
plt.cc: no visible global function definition for ‘par’
plt.cc: no visible global function definition for ‘layout’
plt.indiv: no visible global function definition for ‘plot’
plt.indiv: no visible global function definition for ‘text’
plt.indiv: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘plot’
plt.var: no visible global function definition for ‘points’
plt.var: no visible global function definition for ‘text’
plt.var: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘lines’
rcc: no visible global function definition for ‘var’
rcc: no visible global function definition for ‘cov’
Undefined global functions or variables:
  abline axis box cor cov heat.colors image layout lines par plot
  points text var
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "lines", "par", "plot", "points", "text")
  importFrom("stats", "cor", "cov", "var")
to your NAMESPACE file.
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
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.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’
  All declared Imports should be used.
Found the following significant warnings:
  ./MCMC_prob.h:2091:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/CCMnet.Rcheck/00install.out’ for details.
File ‘CCMnet/libs/CCMnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(cctools)
  > 
  > test_check("cctools")
  ── 1. Failure: Simulation works (@test-usb.R#28)  ──────────────────────────────
  max(abs(rusb(500, quasi = TRUE, theta = 0.99, nu = 1))) is not strictly more than 0.95. Difference: -0.000409
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 36 SKIPPED: 1 FAILED: 1
  1. Failure: Simulation works (@test-usb.R#28) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
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  6.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.4Mb
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  6.2Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
File ‘cec2005benchmark/libs/cec2005benchmark.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 11.5Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.7Mb
    libs   6.3Mb
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.
Namespace in Imports field not imported from: ‘knitr’
  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.
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.
src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
  src/Makevars.in: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
  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).
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.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tools’
  All declared Imports should be used.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
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: ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘circlize’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘bibtex’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinyBS’
  All declared Imports should be used.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
Running examples in ‘CLA-Ex.R’ failed
The error most likely occurred in:

> ### Name: findMu
> ### Title: Find mu(W) and W, given sigma(W) and CLA result
> ### Aliases: findMu
> ### Keywords: optimize arith
> 
> ### ** Examples
> 
> data(muS.sp500)
> ## Full data taking too much time for example
> set.seed(2016)
> iS <- sample.int(length(muS.sp500$mu), 17)
> cov17 <- muS.sp500$covar[iS, iS]
> CLsp.17 <- CLA(muS.sp500$mu[iS], covar=cov17, lB=0, uB = 1/2)
> CLsp.17 # 16 turning points
Call: CLA(mu = muS.sp500$mu[iS], covar = cov17, lB = 0, uB = 1/2)
Critical Line Algorithm for n = 17 assets, resulting in  17  turning points
Overview of result parts:
List of 5
 $ weights_set : num [1:17, 1:17] 0 0 0 0 0 0.5 0 0 0 0 ...
 $ free_indices:List of 17
 $ gammas      : num [1:17] NA -0.01915 -0.01915 -0.01018 -0.00242 ...
 $ lambdas     : num [1:17] NA 3.242 3.242 1.884 0.519 ...
 $ MS_weights  : num [1:17, 1:2] 0.0395 0.0395 0.0395 0.0395 0.0256 ...
> summary(tpS <- CLsp.17$MS_weights[,"Sig"])
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
0.01673 0.01768 0.02042 0.02421 0.02555 0.03946 
> str(s0 <- seq(0.0186, 0.0477, by = 0.0001))
 num [1:292] 0.0186 0.0187 0.0188 0.0189 0.019 0.0191 0.0192 0.0193 0.0194 0.0195 ...
> mu.. <- findMu(s0, result=CLsp.17, covar=cov17)
Error in FUN(X[[i]], ...) : Sig0 must be in [0.0167274, 0.0394623]
Calls: findMu -> lapply -> FUN
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Files which contain pragma(s) suppressing diagnostics:
  ‘src/cld_3/protos/feature_extractor.pb.h’
  ‘src/cld_3/protos/sentence.pb.h’ ‘src/cld_3/protos/task_spec.pb.h’
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    libs  23.5Mb
File ‘clere/libs/clere.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘scales’ ‘sp’
  All declared Imports should be used.
Running ‘testthat.R’ [7s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(clhs)
  > 
  > test_check("clhs")
  ── 1. Failure: basic clhs on a data.frame works (@test-clhs-data.frame.R#15)  ──
  `res` not equal to c(188, 657, 140, 301, 817).
  5/5 mismatches (average diff: 210)
  [1]  97 - 188 == -91
  [2] 903 - 657 == 246
  [3] 539 - 140 == 399
  [4] 451 - 301 == 150
  [5] 979 - 817 == 162
  
  ── 2. Failure: DLHS method on a data.frame works (@test-method_DLHS.R#17)  ─────
  `res` not equal to c(214, 40, 702, 919, 521).
  5/5 mismatches (average diff: 211)
  [1] 412 - 214 ==  198
  [2] 170 -  40 ==  130
  [3] 196 - 702 == -506
  [4] 820 - 919 ==  -99
  [5] 641 - 521 ==  120
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 4 SKIPPED: 0 FAILED: 2
  1. Failure: basic clhs on a data.frame works (@test-clhs-data.frame.R#15) 
  2. Failure: DLHS method on a data.frame works (@test-method_DLHS.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Namespaces in Imports field not imported from:
  ‘emmeans’ ‘utils’
  All declared Imports should be used.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
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.
File ‘clues/libs/clues.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘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’ ‘infuser’ ‘purrr’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    pdf   2.2Mb
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  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
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.
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.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
File ‘CMF/libs/CMF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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:
  'ComplexHeatmap' 'DT' 'blockseg' 'readr'
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   4.3Mb
Namespace in Imports field not imported from: ‘backports’
  All declared Imports should be used.
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.
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.
Namespaces in Imports field not imported from:
  ‘graphics’ ‘jsonlite’ ‘pander’ ‘rlang’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘memoise’
  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.
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.
Namespaces in Imports field not imported from:
  ‘flashClust’ ‘speedglm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       2.2Mb
    extdata   2.1Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
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  7.0Mb
  sub-directories of 1Mb or more:
    app   2.7Mb
    doc   2.3Mb
installed size is 30.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  29.3Mb
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
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.
Found the following significant warnings:
  Utility.c:162:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:187:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:211:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:392:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:417:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:442:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/CompRandFld.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
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.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
File ‘conditions/libs/conditions.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
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 71.9Mb
  sub-directories of 1Mb or more:
    libs  70.7Mb
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:
  ‘Hmisc’ ‘MASS’ ‘geepack’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘Tutorial_Cleaning_GBIF_data_with_CoordinateCleaner.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

Quitting from lines 131-143 (Tutorial_Cleaning_GBIF_data_with_CoordinateCleaner.Rmd) 
Error: processing vignette 'Tutorial_Cleaning_GBIF_data_with_CoordinateCleaner.Rmd' failed with diagnostics:
undefined columns selected
--- failed re-building ‘Tutorial_Cleaning_GBIF_data_with_CoordinateCleaner.Rmd’

--- re-building ‘Tutorial_Cleaning_PBDB_fossils_with_CoordinateCleaner.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

Loading required package: raster
Loading required package: sp

Attaching package: 'raster'

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

    select

Loading required package: maps
Quitting from lines 117-123 (Tutorial_Cleaning_PBDB_fossils_with_CoordinateCleaner.Rmd) 
Error: processing vignette 'Tutorial_Cleaning_PBDB_fossils_with_CoordinateCleaner.Rmd' failed with diagnostics:
undefined columns selected
--- failed re-building ‘Tutorial_Cleaning_PBDB_fossils_with_CoordinateCleaner.Rmd’

SUMMARY: processing the following files failed:
  ‘Tutorial_Cleaning_GBIF_data_with_CoordinateCleaner.Rmd’
  ‘Tutorial_Cleaning_PBDB_fossils_with_CoordinateCleaner.Rmd’

Error: Vignette re-building failed.
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.
Namespaces in Imports field not imported from:
  ‘profr’ ‘xtable’
  All declared Imports should be used.
installed size is 32.1Mb
  sub-directories of 1Mb or more:
    libs  31.6Mb
Namespace in Imports field not imported from: ‘xtable’
  All declared Imports should be used.
Package in Depends field not imported from: ‘calibrate’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.5Mb
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  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
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’ ‘dplyr’ ‘markdown’ ‘shinyjs’ ‘tidyr’
  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:
  ‘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  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
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.
File ‘coxsei/libs/coxsei.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘grDevices’
  All declared Imports should be used.
installed size is 39.4Mb
  sub-directories of 1Mb or more:
    libs  39.2Mb
File ‘cpgen/libs/cpgen.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
File ‘cqrReg/libs/cqrReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
Note: found 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
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.
Namespace in Imports field not imported from: ‘glue’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  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 23.7Mb
  sub-directories of 1Mb or more:
    libs  22.0Mb
Namespace in Imports field not imported from: ‘qte’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    shp   7.8Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data  10.9Mb
Note: found 59670 marked Latin-1 strings
  Note: found 16 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tea’
  All declared Imports should be used.
installed size is 103.3Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs  99.5Mb
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.
File ‘CUSUMdesign/libs/CUSUMdesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [4s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(cusum)
  > 
  > test_check("cusum")
  ── 1. Failure: Output of Control limit simulation (@test-racusum.R#21)  ────────
  `result` not equal to `expected_results`.
  4/10 mismatches (average diff: 0.893)
  [7]  0.00 - 0.51 == -0.51
  [8]  0.00 - 1.02 == -1.02
  [9]  0.60 - 1.53 == -0.93
  [10] 0.42 - 1.53 == -1.11
  
  ── 2. Failure: Output of alpha simulation (@test-racusum_alpha_sim.R#20)  ──────
  `works` not equal to `expected_results`.
  1/1 mismatches
  [1] 0.023 - 0.025 == -0.002
  
  ── 3. Failure: Output of Control limit simulation (@test_racusum_limit_sim.R#19)
  `works` not equal to `expected_results`.
  1/1 mismatches
  [1] 2.45 - 2.59 == -0.14
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 3 SKIPPED: 0 FAILED: 3
  1. Failure: Output of Control limit simulation (@test-racusum.R#21) 
  2. Failure: Output of alpha simulation (@test-racusum_alpha_sim.R#20) 
  3. Failure: Output of Control limit simulation (@test_racusum_limit_sim.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(cvar)
  > 
  > test_check("cvar")
  ── 1. Failure: garch1c1 related functions work ok (@test-garch.R#24)  ──────────
  `a_pred` has changed from known value recorded in 'a_pred.RDS'.
  Component "dist_sim": Component "RNGstate": Attributes: < Component "kind": Length mismatch: comparison on first 2 components >
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 21 SKIPPED: 0 FAILED: 1
  1. Failure: garch1c1 related functions work ok (@test-garch.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘lattice’
  All declared Imports should be used.
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.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   5.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs   1.1Mb
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.
installed size is 24.9Mb
  sub-directories of 1Mb or more:
    libs  24.1Mb
Namespace in Imports field not imported from: ‘robustbase’
  All declared Imports should be used.
Running examples in ‘D2C-Ex.R’ failed
The error most likely occurred in:

> ### Name: predict,D2C-method
> ### Title: predict if there is a connection between node i and node j
> ### Aliases: predict,D2C-method
> 
> ### ** Examples
> 
> require(RBGL)
Loading required package: RBGL
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 object is masked from ‘package:randomForest’:

    combine

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, colMeans, colSums, 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, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

> require(gRbase)
Loading required package: gRbase
> require(foreach)
Loading required package: foreach
> data(example)
> ## load the D2C object
> testDAG<-new("simulatedDAG",NDAG=1, N=50,noNodes=5,
+            functionType = "linear", seed=1,sdn=c(0.25,0.5))
simulatedDAG: DAG number: 1 generated: #nodes= 5 # edges= 0 # samples= 50 
> ## creates a simulatedDAG object for testing
> plot(testDAG@list.DAGs[[1]])
Error in testDAG@list.DAGs[[1]] : subscript out of bounds
Calls: plot
Execution halted
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
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.
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 15.3Mb
  sub-directories of 1Mb or more:
    java  15.2Mb
Namespace in Imports field not imported from: ‘DatabaseConnectorJars’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   3.7Mb
Namespace in Imports field not imported from: ‘miniUI’
  All declared Imports should be used.
Running ‘testthat.R’ [39s/78s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DataExplorer)
  > 
  > test_check("DataExplorer")
  OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
  OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  ── 1. Failure: .ignoreCat (@test-internal.r#11)  ───────────────────────────────
  as.numeric(.ignoreCat(dt, 0)) not equal to c(1L, 2L, 5L, 10L).
  1/4 mismatches
  [3] 4 - 5 == -1
  
  ── 2. Failure: .ignoreCat (@test-internal.r#12)  ───────────────────────────────
  as.numeric(.ignoreCat(dt, 1)) not equal to c(2L, 5L, 10L).
  1/3 mismatches
  [2] 4 - 5 == -1
  
  ── 3. Failure: .ignoreCat (@test-internal.r#13)  ───────────────────────────────
  as.numeric(.ignoreCat(dt, 2)) not equal to c(5L, 10L).
  1/2 mismatches
  [1] 4 - 5 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 130 SKIPPED: 7 FAILED: 3
  1. Failure: .ignoreCat (@test-internal.r#11) 
  2. Failure: .ignoreCat (@test-internal.r#12) 
  3. Failure: .ignoreCat (@test-internal.r#13) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
.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.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
installed size is 65.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  63.3Mb
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
browse: no visible global function definition for ‘slot’
browse: no visible global function definition for ‘page’
default.options: no visible binding for global variable ‘object.size’
heat.view: no visible global function definition for ‘head’
heat.view: no visible global function definition for ‘tail’
whos: no visible global function definition for ‘slotNames’
whos : <anonymous> : <anonymous>: no visible global function definition
  for ‘slot’
Undefined global functions or variables:
  head object.size page slot slotNames tail
Consider adding
  importFrom("methods", "slot", "slotNames")
  importFrom("utils", "head", "object.size", "page", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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:
  ‘dplyr’ ‘ggplot2’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   6.8Mb
Running examples in ‘DCEM-Ex.R’ failed
The error most likely occurred in:

> ### Name: dcem_train
> ### Title: dcem_train: Part of DCEM package.
> ### Aliases: dcem_train
> 
> ### ** Examples
> 
> # Simulating a mixture of univariate samples from three distributions
> # with mean as 20, 70 and 100 and standard deviation as 10, 100 and 40 respectively.
> sample_uv_data = as.data.frame(c(rnorm(1000, 20, 10), rnorm(500, 70, 100),
+ rnorm(2000, 100, 40)), row=3500)
Warning in as.data.frame.numeric(c(rnorm(1000, 20, 10), rnorm(500, 70, 100),  :
  'row.names' is not a character vector of length 3500 -- omitting it. Will be an error!
> 
> # Randomly shuffle the samples.
> sample_uv_data = as.data.frame(sample_uv_data[sample(1:nrow(sample_uv_data)),],
+ row=nrow(sample_uv_data))
Warning in as.data.frame.numeric(sample_uv_data[sample(1:nrow(sample_uv_data)),  :
  'row.names' is not a character vector of length 3500 -- omitting it. Will be an error!
> 
> # Calling the dcem_train() function on the simulated data with threshold of
> # 0.000001 and iteration count of 1000 respectively.
> sample_uv_out = dcem_train(sample_uv_data, num_clusters = 3, iteration_count = 1000,
+ threshold = 0.000001)
Error in if (mean_diff < threshold) { : 
  missing value where TRUE/FALSE needed
Calls: dcem_train -> dcem_cluster_uv
Execution halted
File ‘dcemriS4/libs/dcemriS4.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘gridExtra’ ‘latticeExtra’
  All declared Imports should be used.
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  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
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 24.3Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
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.
Running examples in ‘degenes-Ex.R’ failed
The error most likely occurred in:

> ### Name: deg
> ### Title: Detection of differentially expressed genes.
> ### Aliases: deg
> 
> ### ** Examples
> 
> X1 = matrix(rnorm(2000, 0, 1), 200, 10)
> X2 = matrix(rnorm(2000, 0, 1), 200, 10)
> index = sample(1:200, 5, replace=FALSE)
> X2[index,] = X2[index,] + 5
> D = deg(X1, X2)
Sun Mar  3 11:51:01 2019
Calculation of Z
Calculation of z
Calculation of the kernel estimator
Calculation of the kernel estimator
Determination of the rejection region
Error in if (integral > single.alpha) c1 <- c : 
  missing value where TRUE/FALSE needed
Calls: deg
Execution halted
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/Delaporte.Rcheck/00install.out’ for details.
installed size is 87.6Mb
  sub-directories of 1Mb or more:
    libs  84.9Mb
File ‘delt/libs/delt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Bootstrapping.CI: no visible global function definition for ‘quantile’
D.Jost: no visible global function definition for ‘read.table’
D.Jost: no visible global function definition for ‘write.table’
Dv.locis.corrected.calc: no visible global function definition for
  ‘p.adjust’
Gst.Nei: no visible global function definition for ‘read.table’
Gst.Nei: no visible global function definition for ‘write.table’
H.out: no visible global function definition for ‘write.table’
Hardy.calc: no visible global function definition for ‘chisq.test’
critical.ci.values: no visible global function definition for
  ‘quantile’
inputformat: no visible global function definition for ‘read.table’
inputformat: no visible global function definition for ‘write.table’
over.all.pops: no visible global function definition for ‘write.table’
p.value.correcture: no visible global function definition for
  ‘p.adjust’
pair.pops: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  chisq.test p.adjust quantile read.table write.table
Consider adding
  importFrom("stats", "chisq.test", "p.adjust", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
File ‘DendSer/libs/DendSer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
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  6.7Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.6Mb
    help   1.4Mb
    libs   1.7Mb
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.
File ‘deTestSet/libs/deTestSet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
File ‘DetSel/libs/DetSel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
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 50.3Mb
  sub-directories of 1Mb or more:
    libs  49.8Mb
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  18.0Mb
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.
Namespace in Imports field not imported from: ‘mgcv’
  All declared Imports should be used.
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.
installed size is  9.4Mb
  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.
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  6.6Mb
  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  6.9Mb
  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 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
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.
Running ‘testthat.R’ [14s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(disclapmix)
  > 
  > test_check("disclapmix")
  ── 1. Failure: simulate (@test-disclapmix.R#152)  ──────────────────────────────
  sim_fit$disclap_parameters not equal to fit_std_int_coef$disclap_parameters.
  5/6 mismatches (average diff: 0.139)
  [1] 0.326 - 0.453 == -0.127
  [2] 0.454 - 0.311 ==  0.142
  [4] 0.337 - 0.224 ==  0.113
  [5] 0.364 - 0.540 == -0.176
  [6] 0.506 - 0.371 ==  0.135
  
  ── 2. Failure: simulate (@test-disclapmix.R#153)  ──────────────────────────────
  sim_fit$y not equal to fit_std_int_coef$y.
  4/6 mismatches (average diff: 1.5)
  [3] 20 - 19 ==  1
  [4] 19 - 20 == -1
  [5] 22 - 20 ==  2
  [6] 20 - 22 == -2
  
  ── 3. Failure: rcpp_find_haplotype_in_matrix (@test-disclapmix.R#209)  ─────────
  33 not equal to find_haplotype_in_matrix(x, x[33L, ]).
  1/1 mismatches
  [1] 33 - 1 == 32
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 50 SKIPPED: 0 FAILED: 3
  1. Failure: simulate (@test-disclapmix.R#152) 
  2. Failure: simulate (@test-disclapmix.R#153) 
  3. Failure: rcpp_find_haplotype_in_matrix (@test-disclapmix.R#209) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
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.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/distrEllipse.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
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  8.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.1Mb
    libs   3.8Mb
Error(s) in re-building vignettes:
--- re-building ‘EDA.Rmd’ using rmarkdown

Attaching package: 'dlookr'

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

    transform


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 167-170 (EDA.Rmd) 
Error: processing vignette 'EDA.Rmd' failed with diagnostics:
Need at least 4 complete observations.
--- failed re-building ‘EDA.Rmd’

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

Attaching package: 'dlookr'

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

    transform


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

Loading required package: DBI
Loading required package: RSQLite
Loading required package: dbplyr

Attaching package: 'dbplyr'

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

    ident, sql

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

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

Attaching package: 'dlookr'

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

    transform


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 ‘transformation.Rmd’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 11.6Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   8.1Mb
File ‘doRedis/libs/doRedis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/dpglasso.Rcheck/00install.out’ for details.
File ‘dpglasso/libs/dpglasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   3.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Found the following significant warnings:
  compnoreggilks.cpp:31:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compnoreggilks.cpp:90:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:32:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:88:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:150:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:207:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:380:8: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/DPWeibull.Rcheck/00install.out’ for details.
File ‘drgee/libs/drgee.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    media       2.2Mb
    shinyapps   2.7Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘utils’
  All declared Imports should be used.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    appinformation   9.6Mb
    media            1.2Mb
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 ‘DSL/libs/DSL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

> ### Name: Olearning_Single
> ### Title: Improved single stage O-learning with cross validation
> ### Aliases: Olearning_Single
> 
> ### ** Examples
> 
> n_cluster=5
> pinfo=10
> pnoise=10
> n_sample=50
> set.seed(3)
> example=make_classification(n_cluster,pinfo,pnoise,n_sample)
> pi=list()
> pi[[2]]=pi[[1]]=rep(1,n_sample)
> modelrbf=Olearning_Single(example$X,example$A,example$R,kernel='rbf',m=3,sigma=0.05)
[1] 0.5
[1] NA
Error in svd(rbind(rho, tau, matrix(alpha), nu)) : 
  infinite or missing values in 'x'
Calls: Olearning_Single -> wsvm -> ipop -> ipop -> svd
Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   5.3Mb
Running ‘testthat.R’ [202s/279s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(dtwclust)
  Loading required package: proxy
  
  Attaching package: 'proxy'
  
  The following objects are masked from 'package:stats':
  
      as.dist, dist
  
  The following object is masked from 'package:base':
  
      as.matrix
  
  Loading required package: dtw
  Loaded dtw v1.20-1. See ?dtw for help, citation("dtw") for use in publication.
  
  dtwclust:
  Setting random number generator to L'Ecuyer-CMRG (see RNGkind()).
  To read the included vignettes type: browseVignettes("dtwclust").
  See news(package = "dtwclust") after package updates.
  > library(foreach)
  > library(testthat)
  > 
  > # coverage for multi-threading might not be possible (?)
  > if (nzchar(Sys.getenv("R_COVR"))) RcppParallel::setThreadOptions(1L)
  > # old reporter for CMD checks
  > options(testthat.default_reporter = "summary")
  > 
  > #' To test in a local machine:
  > #' Sys.setenv(NOT_CRAN = "true"); test_dir("tests/testthat/")
  > #' OR
  > #' devtools::test() # broken, can't figure out why
  > #'
  > #' To disable parallel tests, before calling test() run:
  > #'
  > #'   options(dtwclust_skip_par_tests = TRUE)
  > #'
  > testthat::test_check("dtwclust")
  ── 1. Failure: Cluster reinitialization in partitional tsclust works.  ─────────
  `... <- NULL` did not produce any warnings.
  
  ── 2. Failure: Cluster reinitialization in partitional tsclust works.  ─────────
  pc_cr@converged isn't false.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1889 SKIPPED: 3 FAILED: 2
  1. Failure: Cluster reinitialization in partitional tsclust works. 
  2. Failure: Cluster reinitialization in partitional tsclust works. 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘digest’ ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
installed size is 30.7Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    2.5Mb
    libs  23.6Mb
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.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Running examples in ‘DZEXPM-Ex.R’ failed
The error most likely occurred in:

> ### Name: dzexpm
> ### Title: The estimation and prediction function for the skewed spatial
> ###   processes
> ### Aliases: dzexpm
> 
> ### ** Examples
> 
>   real<- as.matrix(do.call(cbind, MaxTemp03))
>   n_ful<- nrow(real)
>   y_ful<- real[,2]
>   x_ful<- real[,7]
>   x_ful<- log(x_ful)
>   x_ful<- scale(x_ful)
>   u1<- real[,3]
>   u2<- real[,4]
>   theta<- 2/150000
>   n<- 56
>   p<- 0.1
>  dzexpm(y_ful, x_ful, n_ful, n, u1, u2, theta, p, 50, 20)
Error in chol.default(Cpred) : 
  the leading minor of order 19 is not positive definite
Calls: dzexpm -> t -> chol -> chol.default
Execution halted
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
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.
Running examples in ‘easyPubMed-Ex.R’ failed
The error most likely occurred in:

> ### Name: fetch_pubmed_data
> ### Title: Retrieve PubMed Data in XML or TXT Format
> ### Aliases: fetch_pubmed_data
> 
> ### ** Examples
> 
> ## Example 01: retrieve data in TXT format
> library("easyPubMed")
> dami_query_string <- "Damiano Fantini[AU] AND 2018[PDAT]"
> dami_on_pubmed <- get_pubmed_ids(dami_query_string)
> Sys.sleep(1) # avoid server timeout
> dami_papers <- fetch_pubmed_data(dami_on_pubmed, format = "abstract")
Warning in url(efetch_url, open = "rb", encoding = "UTF8") :
  URL 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&WebEnv=NCID_1_48610493_130.14.18.97_9001_1551902314_1622452383_0MetA0_S_MegaStore&query_key=1&retstart=0&retmax=500&rettype=abstract&retmode=text': status was 'Couldn't connect to server'
Error in url(efetch_url, open = "rb", encoding = "UTF8") : 
  cannot open the connection to 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&WebEnv=NCID_1_48610493_130.14.18.97_9001_1551902314_1622452383_0MetA0_S_MegaStore&query_key=1&retstart=0&retmax=500&rettype=abstract&retmode=text'
Calls: fetch_pubmed_data -> url
Execution halted
File ‘ebdbNet/libs/ebdbNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    hac    4.0Mb
Namespace in Imports field not imported from: ‘lubridate’
  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.
File ‘edesign/libs/edesign.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [9s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(edfReader)
  > 
  > test_check("edfReader")
  edfPlusC.edf : Testing header
  edfPlusC.edf : Testing signals
  bdfPlusC.bdf : Testing header
  bdfPlusC.bdf : Testing signals
  edfAnnonC.edf : Testing header
  edfAnnonC.edf : Testing signals
  edfPlusD.edf : Testing header
  edfPlusD.edf : Testing signals
  testASignalsFile edfPlusC.edf 
  testASignalsFile bdfPlusC.bdf 
  testASignalsFile edfPlusD.edf 
  testASignalsFile edfAnnonC.edf 
  ── 1. Failure: A6: A random range 3 (@test20_FromTill.R#162)  ──────────────────
  aSignal$annotations not equal to allAnnots[annotsInRange, ].
  Attributes: < Component "row.names": Mean relative difference: 0.6666667 >
  
  edfPlusC.edf : testOSignalsFile: isContinuous= TRUE 
  bdfPlusC.bdf : testOSignalsFile: isContinuous= TRUE 
  edfPlusD.edf : testOSignalsFile: isContinuous= FALSE 
  edfAnnonC.edf : testOSignalsFile: isContinuous= TRUE 
  edfPlusC.edf : min/max tests
  bdfPlusC.bdf : min/max tests
  edfPlusD.edf : min/max tests
  edfAnnonC.edf : min/max tests
  edfPlusC.edf : signal selection tests
  bdfPlusC.bdf : signal selection tests
  edfPlusD.edf : signal selection tests
  edfAnnonC.edf : signal selection tests
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 790 SKIPPED: 0 FAILED: 1
  1. Failure: A6: A random range 3 (@test20_FromTill.R#162) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
File ‘EDR/libs/EDR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘test-all.R’ [20s/46s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(eeptools)
  Loading required package: ggplot2
  > 
  > test_check("eeptools")
  OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
  OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  ── 1. Failure: statamode returns correct modes for each method using numbers (@t
  `d` not equal to 4.
  1/1 mismatches
  [1] 7 - 4 == 3
  
  ── 2. Failure: statamode handles all types of modes (@test-statamode.r#128)  ───
  statamode(vecA, method = tests[i, "method"]) not equal to "B".
  1/1 mismatches
  x[1]: "F"
  y[1]: "B"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 517 SKIPPED: 0 FAILED: 2
  1. Failure: statamode returns correct modes for each method using numbers (@test-statamode.r#24) 
  2. Failure: statamode handles all types of modes (@test-statamode.r#128) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
installed size is 116.3Mb
  sub-directories of 1Mb or more:
    libs  115.6Mb
Running examples in ‘egonet-Ex.R’ failed
The error most likely occurred in:

> ### Name: egonet-package
> ### Title: Tool for ego-centric measures in Social Network Analysis
> ### Aliases: egonet-package egonet
> ### Keywords: package
> 
> ### ** Examples
> 
> ## This is a list of file' names containing the ego-network
> ff <- c("q1.csv","q2.csv","q3.csv")
> files  <- paste("http://www.egonet.associazionerospo.org/egonetdata/",ff,sep="")
> names(files) <- ff
> 
> ##if all your data are in a directory (eg. egonets, containing all files with the same extension), 
> ##you can easily get this list with the following commands
> # ff <- dir("./egonets",pattern=".csv")
> # files  <- paste("./egonets/",ff,sep="")
> # names(files) <- ff
> 
> 
> # Here is a dataset with demographic informations and the names of files containing the ego-network
> #we now want to add network indeces to this data.frame
> data <- data.frame( gender=c("F","F","M"), age =(2:4)*10, filename=ff)
> data
  gender age filename
1      F  20   q1.csv
2      F  30   q2.csv
3      M  40   q3.csv
> 
> 
> #import all the egonets
> mats <- lapply(files,read.egonet)
Error in `[.data.frame`(dat, , ego.name) : undefined columns selected
Calls: lapply -> FUN -> [ -> [.data.frame -> [ -> [.data.frame
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(EGRETci)
  > test_check("EGRETci")
  ── 1. Failure: blockSample (@tests_boot_tests.R#72)  ───────────────────────────
  bsReturn$ConcLow[1] not equal to 0.62.
  1/1 mismatches
  [1] 1.4 - 0.62 == 0.78
  
  ── 2. Failure: blockSample (@tests_boot_tests.R#73)  ───────────────────────────
  bsReturn$Date[1] not equal to as.Date("1979-10-24").
  Mean relative difference: 0.01158621
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 17 SKIPPED: 5 FAILED: 2
  1. Failure: blockSample (@tests_boot_tests.R#72) 
  2. Failure: blockSample (@tests_boot_tests.R#73) 
  
  Error: testthat unit tests failed
  Execution halted
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.
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.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data  11.5Mb
Error(s) in re-building vignettes:
--- re-building ‘ellipticpaper.Rnw’ using Sweave

Attaching package: ‘elliptic’

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

    sd, sigma

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

    is.primitive

Loading required package: emulator
Loading required package: mvtnorm
Loading required package: calibrator

Error: processing vignette 'ellipticpaper.Rnw' failed with diagnostics:
 chunk 62 (label = mle_calc) 
Error in stats::optim(par = par, fn = fn, control = list(fnscale = -1)) : 
  function cannot be evaluated at initial parameters

--- failed re-building ‘ellipticpaper.Rnw’

--- re-building ‘residuetheorem.Rnw’ using Sweave

Attaching package: ‘elliptic’

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

    sd, sigma

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

    is.primitive

--- finished re-building ‘residuetheorem.Rnw’

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

Error: Vignette re-building failed.
Execution halted
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 ‘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.
Running ‘testthat.R’ [17s/86s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (packageVersion("testthat") >= "0.9.1") {
  +   library(testthat)
  +   test_check("emil")
  + }
  Loading required package: emil
  
  Attaching package: 'emil'
  
  The following object is masked from 'package:base':
  
      mode
  
  ── 1. Failure: k-NN imputation (@test-preprocess.r#30)  ────────────────────────
  sets$test$x[na.ind] not equivalent to ifelse(na.ind[, 2] <= 3, 5, 4.5).
  3/10 mismatches (average diff: 0.5)
  [5]  5 - 4.5 == 0.5
  [7]  5 - 4.5 == 0.5
  [10] 5 - 4.5 == 0.5
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 183 SKIPPED: 1 FAILED: 1
  1. Failure: k-NN imputation (@test-preprocess.r#30) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  17.4Mb
File ‘emIRT/libs/emIRT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    extdata  10.2Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    xsd   5.4Mb
'library' or 'require' calls to packages already attached by Depends:
  ‘clusterSim’ ‘earth’
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘clusterSim’ ‘earth’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.5Mb
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  7.1Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.5Mb
Note: found 23639 marked Latin-1 strings
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    lib    3.5Mb
    libs   1.1Mb
Namespaces in Imports field not imported from:
  ‘git2r’ ‘servr’
  All declared Imports should be used.
File ‘endogMNP/libs/endogMNP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘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:
  ‘BiocParallel’ ‘broom’ ‘reshape2’ ‘rmarkdown’
  All declared Imports should be used.
File ‘enviPat/libs/enviPat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    doc    3.3Mb
    help   3.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘ROCR’ ‘c060’ ‘methods’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘colorspace’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘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.
Found the following significant warnings:
  motor_param.cpp:257:5: warning: explicitly assigning value of variable of type 'arma::vec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/episode.Rcheck/00install.out’ for details.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘testthat’ ‘tidyr’
  All declared Imports should be used.
Found the following significant warnings:
  utilities.c:175:32: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/Equalden.HD.Rcheck/00install.out’ for details.
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.
Namespace in Imports field not imported from: ‘signal’
  All declared Imports should be used.
File ‘esaddle/libs/esaddle.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
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 28.7Mb
  sub-directories of 1Mb or more:
    libs  28.4Mb
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.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘msm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘EnvStats’
  All declared Imports should be used.
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.
File ‘evolqg/libs/evolqg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘polynom’
  All declared Imports should be used.
print.cdf : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.cdf: warning in get("x", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.cdf: warning in get("y", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.ogive : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.ogive: warning in get("x", env = environment(x)): partial
  argument match of 'env' to 'envir'
print.ogive: warning in get("y", env = environment(x)): partial
  argument match of 'env' to 'envir'
quantile.expert: warning in formatC(paste(100 * probs, "%", sep = ""),
  format = "fg", wid = 1, digits = dig): partial argument match of
  'wid' to 'width'
MS: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
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.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘mlbench’ ‘parallel’
  All declared Imports should be used.
Running ‘testthat.R’ [4s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fabricatr)
  > 
  > test_check("fabricatr")
  ── 1. Failure: Multi-level Resample validity (@test-resampling.R#155)  ─────────
  length(unique(split(resample_validity$cities, rep(1:6, each = 5)))) not equal to 6.
  1/1 mismatches
  [1] 5 - 6 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 363 SKIPPED: 1 FAILED: 1
  1. Failure: Multi-level Resample validity (@test-resampling.R#155) 
  
  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.
Namespace in Imports field not imported from: ‘pkgbuild’
  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 ‘farff/libs/farff.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
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  5.2Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.0Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Namespace in Imports field not imported from: ‘RobustGaSP’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
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 18.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  17.1Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.2Mb
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  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/data/gannet/ripley/R/packages/tests-clang/FastRWeb.Rcheck/00install.out’ for details.
Output from running autoconf:
  configure.ac:36: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
  ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
  ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from...
  ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from...
  ../../lib/autoconf/c.m4:1444: AC_C_BIGENDIAN is expanded from...
  configure.ac:36: the top level
Note: information on .o files is not available
File ‘FastRWeb/libs/null.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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  5.5Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.8Mb
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.
File ‘fbroc/libs/fbroc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is 57.6Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  54.5Mb
Running examples in ‘fdapace-Ex.R’ failed
The error most likely occurred in:

> ### Name: CreateBWPlot
> ### Title: Functional Principal Component Analysis Bandwidth Diagnostics
> ###   plot
> ### Aliases: CreateBWPlot
> 
> ### ** Examples
> 
> set.seed(1)
> n <- 20
> pts <- seq(0, 1, by=0.05)
> sampWiener <- Wiener(n, pts)
> sampWiener <- Sparsify(sampWiener, pts, 10)
> res1 <- FPCA(sampWiener$Ly, sampWiener$Lt, 
+             list(dataType='Sparse', error=FALSE, kernel='epan', verbose=FALSE))
> CreateBWPlot(res1)
Error in value[[3L]](cond) : 
  Multiplier : 0.5 failed to return valid FPCA object. Change multiplier values.
Calls: CreateBWPlot ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.4Mb
File ‘fdaPDE/libs/fdaPDE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   7.4Mb
File ‘FDGcopulas/libs/FDGcopulas.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
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.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rvest’ ‘stringi’
  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.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Namespace in Imports field not imported from: ‘pROC’
  All declared Imports should be used.
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.
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: ‘rappdirs’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘mapproj’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.2Mb
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.
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  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
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  6.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
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 11.7Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
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
File ‘flsa/libs/flsa.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.5Mb
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
File ‘FME/libs/FME.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘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.
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.
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  9.1Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   5.4Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
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 78.0Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs  76.3Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   6.7Mb
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  8.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    2.1Mb
installed size is 39.7Mb
  sub-directories of 1Mb or more:
    libs  39.2Mb
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.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
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 ‘FTRLProximal/libs/FTRLProximal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [12s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(funData)
  
  Attaching package: 'funData'
  
  The following object is masked from 'package:stats':
  
      integrate
  
  > 
  > test_check("funData")
  ── 1. Failure: sparsify (@test_simulation.R#219)  ──────────────────────────────
  nObsPoints(s) not equal to c(2, 2).
  1/2 mismatches
  [2] 3 - 2 == 1
  
  ── 2. Failure: sparsify (@test_simulation.R#220)  ──────────────────────────────
  argvals(s) not equal to list(c(0.57, 0.7), c(0.94, 0.95)).
  Component 1: Mean relative difference: 0.1360544
  Component 2: Numeric: lengths (3, 2) differ
  
  ── 3. Failure: sparsify (@test_simulation.R#221)  ──────────────────────────────
  X(s) not equal to list(c(1.17678, -2.76915), c(-2.40195, -2.32616)).
  Component 1: Mean relative difference: 0.7422477
  Component 2: Numeric: lengths (3, 2) differ
  
  ── 4. Failure: sparsify (@test_simulation.R#227)  ──────────────────────────────
  as.irregFunData(s[[1]])@argvals not equal to list(4, 2).
  Component 1: Mean relative difference: 1
  Component 2: Numeric: lengths (2, 1) differ
  
  ── 5. Failure: sparsify (@test_simulation.R#228)  ──────────────────────────────
  as.irregFunData(s[[1]])@X not equal to list(4, 3).
  Component 1: Mean relative difference: 1
  Component 2: Numeric: lengths (2, 1) differ
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 488 SKIPPED: 0 FAILED: 5
  1. Failure: sparsify (@test_simulation.R#219) 
  2. Failure: sparsify (@test_simulation.R#220) 
  3. Failure: sparsify (@test_simulation.R#221) 
  4. Failure: sparsify (@test_simulation.R#227) 
  5. Failure: sparsify (@test_simulation.R#228) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘funHDDC-Ex.R’ failed
The error most likely occurred in:

> ### Name: predict.funHDDC
> ### Title: Predict new results from a funHDDC model
> ### Aliases: predict.funHDDC
> 
> ### ** Examples
> 
> ##Univariate example
>     data("trigo")
>     basis<- create.bspline.basis(c(0,1), nbasis=25)
>     z<-sample(1:100,0.8*100,replace=FALSE)
>     var1_train<-smooth.basis(argvals=seq(0,1,length.out = 100),y=t(trigo[z,1:100]),
+                              fdParobj=basis)$fd
>     var1_test<-smooth.basis(argvals=seq(0,1,length.out = 100),y=t(trigo[-z,1:100]),
+                             fdParobj=basis)$fd
> 
>     model<-funHDDC(var1_train,K=2)
      model K threshold complexity         BIC
1 AKJBKQKDK 2       0.2        103 -373,867.94

SELECTED: model  AKJBKQKDK  with  2  clusters.
Selection Criterion: BIC.
>     pred<-predict(model,var1_test)
> 
> ##Multivariate example
>     data("triangle")
>     basis<- create.bspline.basis(c(1,21), nbasis=25)
>     z<-sample(1:100,0.8*100,replace=FALSE)
>     var1_train<-smooth.basis(argvals=seq(1,21,length.out = 101),y=t(triangle[z,1:101]),
+                               fdParobj=basis)$fd
>     var1_test<-smooth.basis(argvals=seq(1,21,length.out = 101),y=t(triangle[-z,1:101]),
+                             fdParobj=basis)$fd
>     var2_train<-smooth.basis(argvals=seq(1,21,length.out = 101),y=t(triangle[z,102:202]),
+                             fdParobj=basis)$fd
>     var2_test<-smooth.basis(argvals=seq(1,21,length.out = 101),y=t(triangle[-z,102:202]),
+                             fdParobj=basis)$fd
> 
>     model<-funHDDC(list(var1_train,var2_train),K=3)
Warning in funHDDC(list(var1_train, var2_train), K = 3) :
  All models diverged.
>     pred<-predict(model,list(var1_test,var2_test))
Error in UseMethod("predict") : 
  no applicable method for 'predict' applied to an object of class "list"
Calls: predict
Execution halted
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  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
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
Namespaces in Imports field not imported from:
  ‘future’ ‘utils’
  All declared Imports should be used.
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  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.3Mb
File ‘gaselect/libs/gaselect.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   9.2Mb
installed size is 118.4Mb
  sub-directories of 1Mb or more:
    libs  117.9Mb
Namespaces in Imports field not imported from:
  ‘methods’ ‘rstantools’
  All declared Imports should be used.
installed size is 86.9Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     83.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  16.9Mb
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 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
Found the following significant warnings:
  cGetHCS.c:9:33: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  cIdentical.c:9:34: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/gdmp.Rcheck/00install.out’ for details.
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.
File ‘GEEaSPU/libs/GEEaSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(httr)
  > library(genderizeR)
  
  Welcome to genderizeR package version: 2.0.0
  
  Homepage: http://www.wais.kamil.rzeszow.pl/genderizeR
  
  Changelog: news(package = 'genderizeR')
  Help & Contact: help(genderizeR)
  
  If you find this package useful cite it please. Thank you! 
  See: citation('genderizeR')
  
  To suppress this message use:
  suppressPackageStartupMessages(library(genderizeR))
  > 
  > test_check("genderizeR")
  ── 1. Failure: classificationErrors (@test.R#63)  ──────────────────────────────
  ...$NULL not equal to 0.6521739.
  1/1 mismatches
  [1] 0.617 - 0.652 == -0.0352
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 23 SKIPPED: 2 FAILED: 1
  1. Failure: classificationErrors (@test.R#63) 
  
  Error: testthat unit tests failed
  Execution halted
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 11.0Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
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.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    exdata   5.1Mb
File ‘genMOSSplus/libs/genMOSSplus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘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.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   5.1Mb
File ‘geoCount/libs/geoCount.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   3.7Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   6.2Mb
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    data  26.0Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R         6.1Mb
    extdata   1.4Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  13.0Mb
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
Found the following assignments to the global environment:
File ‘geoR/R/auxiliar.R’:
  assign(".objfuncQQ", objfunc, pos = 1)
  assign(".bounds.list", .bounds.list, pos = 1)
  assign("madtonormalQQ", madtonormalQQ, pos = 1)
File ‘geoR/R/likGRF.R’:
  assign(".likGRF.dists.vec", lapply(split(as.data.frame(coords), 
    realisations), vecdist), pos = 1)
  assign(".likGRF.dists.vec", lapply(split(as.data.frame(coords), 
    realisations), vecdist), pos = 1)
  assign(".likGRF.dists.vec", lapply(split(as.data.frame(coords.c), 
    temp.list$realisations), vecdist), pos = 1)
  assign(".temp.lower.lambda", -2, pos = 1)
  assign(".temp.upper.lambda", 2, pos = 1)
File ‘geoR/R/profiles.R’:
  assign(".temp.list", list(n = n, z = data, beta.size = dim(trend)[2], 
    kappa = obj.likfit$kappa, xmat = trend, method.lik = obj.likfit$method.lik, 
    dists.lowertri = dists.vec, cov.model = obj.likfit$cov.model, 
    fix.lambda = obj.likfit$transform.info$fix.lambda, lambda = obj.likfit$lambda, 
    lower.phi = lower.phi, upper.phi = upper.phi, lower.sigmasq = lower.sigmasq, 
    phi.est = phi, tausq.rel.est = tausq.rel, tausq.est = tausq, 
    sigmasq.est = sigmasq), pos = 1)
  assign(".temp.temp.list", get(".temp.list", pos = 1), pos = 1)
  assign(".temp.list", .temp.temp.list, pos = 1)
  assign(".temp.lambda", lambda, pos = 1)
  assign(".temp.lambda", lambda, pos = 1)
File ‘geoR/R/simul.R’:
  assign("setRF", geoR2RF(cov.model = cov.model, cov.pars = cov.pars, 
    nugget = nugget, kappa = kappa, aniso.pars = aniso.pars), 
    pos = 1)
File ‘geoR/R/variofit.R’:
  assign(".temp.theta", NULL, pos = 1)
  assign(".temp.theta", theta, pos = 1)
  assign(".IND.geoR.variog.model.env", TRUE, pos = 1)
File ‘geoR/R/variogram.R’:
  assign(".variog4.nomessage", TRUE, pos = 1)
File ‘geoR/libs/geoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
Running examples in ‘geotopbricks-Ex.R’ failed
The error most likely occurred in:

> ### Name: create.geotop.inpts.keyword
> ### Title: Creates an 'geotop.inpts' files the keyword and their values of
> ###   a date.frame like the one returned by
> ###   'declared.geotop.inpts.keywords'
> ### Aliases: create.geotop.inpts.keyword
> 
> ### ** Examples
> 
> 
> library(geotopbricks)
> 
> #Simulation working path
> wpath <- 'http://www.rendena100.eu/public/geotopbricks/simulations/panola13_run2xC_test3'
> df <- declared.geotop.inpts.keywords(wpath=wpath)
Warning in file(con, "r") :
  URL 'http://www.rendena100.eu/public/geotopbricks/simulations/panola13_run2xC_test3/geotop.inpts': status was 'Failure when receiving data from the peer'
Error in file(con, "r") : 
  cannot open the connection to 'http://www.rendena100.eu/public/geotopbricks/simulations/panola13_run2xC_test3/geotop.inpts'
Calls: declared.geotop.inpts.keywords -> <Anonymous> -> file
Execution halted
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘utils’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘shinydashboard’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘gitrd-vignette-introduction.Rmd’ using rmarkdown
Quitting from lines 99-112 (gitrd-vignette-introduction.Rmd) 
Error: processing vignette 'gitrd-vignette-introduction.Rmd' failed with diagnostics:
cannot open URL 'http://www.rad.cvm.gov.br/enetconsulta/frmDownloadDocumento.aspx?CodigoInstituicao=2&NumeroSequencialDocumento=2108'
--- failed re-building ‘gitrd-vignette-introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘bitops’ ‘data.table’ ‘dplyr’ ‘httr’
  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.
Found the following significant warnings:
  FORCE_certify.c:116:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/GFORCE.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘plotly’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggforce’ ‘plyr’
  All declared Imports should be used.
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
Namespaces in Imports field not imported from:
  ‘GGEBiplotGUI’ ‘gge’ ‘utils’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   2.7Mb
Running ‘test-all.R’ [82s/186s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check('ggfortify')
  Loading required package: ggfortify
  Loading required package: ggplot2
  initial  value 7.505733 
  final  value 7.505688 
  converged
  Initial stress        : 0.01705
  stress after  10 iters: 0.00951, magic = 0.500
  stress after  20 iters: 0.00941, magic = 0.500
  initial  value 7.505733 
  final  value 7.505688 
  converged
  Initial stress        : 0.01705
  stress after  10 iters: 0.00951, magic = 0.500
  stress after  20 iters: 0.00941, magic = 0.500
  ── 1. Failure: fortify.glmnet works for Orange (@test-glmnet.R#33)  ────────────
  dim(fortified) not equal to c(57, 5).
  1/2 mismatches
  [1] 56 - 57 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1451 SKIPPED: 9 FAILED: 1
  1. Failure: fortify.glmnet works for Orange (@test-glmnet.R#33) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘lazyeval’ ‘readr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘grid’ ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggforce’ ‘webshot’ ‘ztable’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: ‘__var_41_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/gglasso.Rcheck/00install.out’ for details.
Running examples in ‘GGMM-Ex.R’ failed
The error most likely occurred in:

> ### Name: BRGM
> ### Title: Learning gene regulatory networks for breast cancer.
> ### Aliases: BRGM
> ### Keywords: BRGM
> 
> ### ** Examples
> 
>  ## Don't show: 
> set.seed(10)
> library(GGMM)
> data(breast)
> Gra <- BRGM(breast[1:50,1:5], M=2,alpha1 = 0.5, alpha2 = 0.8, alpha3 = 0.9, iteration = 1, warm = 0)
working subdata size=10
Read 25 items
Read 30 items
working subdata size=10
The given q-threshold value is too small
Warning in file(file, "r") :
  cannot open file 'sim0.pcor.est.ini': No such file or directory
Error in file(file, "r") : cannot open the connection
Calls: BRGM -> psical -> matrix -> scan -> file
Execution halted
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grid’ ‘scales’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘reshape2’ ‘viridisLite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
  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’ ‘Hmisc’ ‘colourpicker’ ‘dplyr’ ‘ggpmisc’ ‘ggrepel’
  ‘grDevices’ ‘gridExtra’ ‘lazyeval’ ‘markdown’ ‘plotly’ ‘quantreg’
  ‘rlang’ ‘shinyjs’ ‘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  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.2Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
Namespaces in Imports field not imported from:
  ‘reshape2’ ‘rosm’
  All declared Imports should be used.
File ‘ghyp/libs/ghyp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
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  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
File ‘glcm/libs/glcm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

> ### Name: test_raster
> ### Title: Randomly generated 100x100 test image
> ### Aliases: test_raster
> 
> ### ** Examples
> 
> # The image was generated with the following code:
> require(raster)
Loading required package: raster
Loading required package: sp
> set.seed(0)
> test_matrix <- matrix(runif(100)*32, nrow=10)
> test_raster <- raster(test_matrix, crs='+init=EPSG:4326')
Error in CRS(as.character(projection(crs))) : no system list, errno: 2
Calls: raster ... raster -> .local -> raster -> raster -> .local -> CRS
Execution halted
File ‘GLDEX/libs/GLDEX.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘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 29.0Mb
  sub-directories of 1Mb or more:
    libs  28.6Mb
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.
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.
File ‘glmlep/libs/glmlep.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/glmmfields.Rcheck/00install.out’ for details.
installed size is 54.2Mb
  sub-directories of 1Mb or more:
    libs  53.3Mb
installed size is 48.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  46.2Mb
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.
Namespaces in Imports field not imported from:
  ‘rworldmap’ ‘shape’
  All declared Imports should be used.
Running ‘test-all.R’ [53s/128s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > library("GMCM")
  > 
  > test_check("GMCM")
  ── 1. Error: EMAlgorithm returns properly formatted output (@test-EMAlgorithm.R#
  Delta likelihood was negative. Something went wrong!
  1: suppressWarnings({
         res <- GMCM:::EMAlgorithm(dat$z, m = m, max.ite = 100, trace.theta = trace_theta)
     }) at testthat/test-EMAlgorithm.R:12
  2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  3: GMCM:::EMAlgorithm(dat$z, m = m, max.ite = 100, trace.theta = trace_theta) at testthat/test-EMAlgorithm.R:13
  4: stop("Delta likelihood was negative. Something went wrong!") at /data/gannet/ripley/R/packages/tests-clang/GMCM/R/EMAlgortihm.R:88
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2172 SKIPPED: 2 FAILED: 1
  1. Error: EMAlgorithm returns properly formatted output (@test-EMAlgorithm.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘gMWT/libs/gMWT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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  5.7Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    4.0Mb
installed size is 27.8Mb
  sub-directories of 1Mb or more:
    R  27.6Mb
File ‘gRain/libs/gRain.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
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 14.3Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
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 18.2Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
File ‘growcurves/libs/growcurves.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
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  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Namespace in Imports field not imported from: ‘rrcov’
  All declared Imports should be used.
Missing or unexported object: ‘cellWise::DetectDeviatingCells’
File ‘GSE/libs/GSE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

> ### Name: TSGS
> ### Title: Two-Step Generalized S-Estimator for cell- and case-wise
> ###   outliers
> ### Aliases: TSGS
> 
> ### ** Examples
> 
> set.seed(12345)
> 
> # Generate 5% cell-wise contaminated normal data
> # using a random correlation matrix with condition number 100
> x <- generate.cellcontam(n=100, p=10, cond=100, contam.size=5, contam.prop=0.05)
> 
> ## Using MLE
> slrt( cov(x$x), x$A)
[1] 69.01395
> 
> ## Using Fast-S
> slrt( rrcov:::CovSest(x$x)@cov, x$A)
[1] 44.9836
> 
> ## Using 2SGS
> slrt( TSGS(x$x)@S, x$A)
Error: 'DetectDeviatingCells' is not an exported object from 'namespace:cellWise'
Execution halted
File ‘gsl/libs/gsl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
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.
Namespace in Imports field not imported from: ‘urca’
  All declared Imports should be used.
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.
Error(s) in re-building vignettes:
--- re-building ‘gwqs-vignette.Rmd’ using rmarkdown
Welcome to package ztable ver 0.2.0
Quitting from lines 118-128 (gwqs-vignette.Rmd) 
Error: processing vignette 'gwqs-vignette.Rmd' failed with diagnostics:
There are no negative b1 in the bootstrapped models
--- failed re-building ‘gwqs-vignette.Rmd’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 125.2Mb
  sub-directories of 1Mb or more:
    java  123.3Mb
File ‘hapassoc/libs/hapassoc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
Found the following significant warnings:
  HARDataCreationC.cpp:19:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/HARModel.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [31s/69s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(harvestr)
  > foreach::registerDoSEQ()
  > test_check("harvestr")
  ── 1. Failure: gather gives the appropriate kinds of seed. (@test-gather.R#42)  
  RNGkind() not identical to c("L'Ecuyer-CMRG", "Inversion").
  Lengths differ: 3 is not 2
  
  ── 2. Failure: gather replaces seed. (@test-gather.R#57)  ──────────────────────
  RNGkind() not identical to c("Mersenne-Twister", "Box-Muller").
  Lengths differ: 3 is not 2
  
  ── 3. Failure: get.seed retrieves properly (@test-seeds.R#14)  ─────────────────
  `seed` not identical to `eseed`.
  Mean relative difference: 0.9608917
  
  ── 4. Failure: replace.seed (@test-seeds.R#29)  ────────────────────────────────
  `k` not identical to c("Mersenne-Twister", "Box-Muller").
  Lengths differ: 3 is not 2
  
  ── 5. Failure: replace.seed (@test-seeds.R#30)  ────────────────────────────────
  `l` not identical to c("L'Ecuyer-CMRG", "Inversion").
  Lengths differ: 3 is not 2
  
  ── 6. Failure: withseed replaces previous seed. (@test-seeds.R#56)  ────────────
  RNGkind() not identical to c("Mersenne-Twister", "Box-Muller").
  Lengths differ: 3 is not 2
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 119 SKIPPED: 5 FAILED: 6
  1. Failure: gather gives the appropriate kinds of seed. (@test-gather.R#42) 
  2. Failure: gather replaces seed. (@test-gather.R#57) 
  3. Failure: get.seed retrieves properly (@test-seeds.R#14) 
  4. Failure: replace.seed (@test-seeds.R#29) 
  5. Failure: replace.seed (@test-seeds.R#30) 
  6. Failure: withseed replaces previous seed. (@test-seeds.R#56) 
  
  Error: testthat unit tests failed
  Execution halted
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.
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
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 10.1Mb
  sub-directories of 1Mb or more:
    data  10.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   1.3Mb
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 23.4Mb
  sub-directories of 1Mb or more:
    libs  23.0Mb
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  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Running examples in ‘hetGP-Ex.R’ failed
The error most likely occurred in:

> ### Name: LOO_preds
> ### Title: Leave one out predictions
> ### Aliases: LOO_preds
> 
> ### ** Examples
> 
> set.seed(32)
> ## motorcycle data
> library(MASS)
> X <- matrix(mcycle$times, ncol = 1)
> Z <- mcycle$accel
> nvar <- 1
> 
> ## Model fitting
> model <- mleHomGP(X = X, Z = Z, lower = rep(0.1, nvar), upper = rep(10, nvar),
+                   covtype = "Matern5_2", known = list(beta0 = 0))
Error in chol.default(C + diag(eps + g/mult)) : 
  the leading minor of order 4 is not positive definite
Error in matern5_2_1args(X1 * rep(1/theta, rep(nrow(X1), length(theta)))) : 
  Not a matrix.
Calls: mleHomGP ... add_diag -> cov_gen -> cov_Matern5_2 -> matern5_2_1args
Execution halted
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.
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.
File ‘hier.part/libs/hier.part.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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  8.9Mb
  sub-directories of 1Mb or more:
    highlight   1.1Mb
    libs        7.7Mb
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.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
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  6.2Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   4.3Mb
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  7.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   4.1Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’
  All declared Imports should be used.
File ‘HotDeckImputation/libs/HotDeckImputation.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
Found the following significant warnings:
  sar.cpp:210:32: warning: explicitly assigning value of variable of type 'arma::sp_mat' (aka 'SpMat<double>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/HSAR.Rcheck/00install.out’ for details.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
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 ‘hSDM/libs/hSDM.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘useful.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Objects: ‘hSDM.Nmixture.o’, ‘hSDM.Nmixture.iCAR.o’, ‘hSDM.ZIB.o’,
      ‘hSDM.ZIB.iCAR.alteration.o’, ‘hSDM.ZIB.iCAR.o’, ‘hSDM.ZIP.o’,
      ‘hSDM.ZIP.iCAR.alteration.o’, ‘hSDM.ZIP.iCAR.o’,
      ‘hSDM.binomial.o’, ‘hSDM.binomial.iCAR.o’, ‘hSDM.poisson.o’,
      ‘hSDM.poisson.iCAR.o’, ‘hSDM.siteocc.o’, ‘hSDM.siteocc.iCAR.o’
File ‘hSDM/libs/hSDM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor 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 ‘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.
File ‘htdp/libs/htdp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  language.c:41:5: warning: flexible array initialization is a GNU extension [-Wgnu-flexible-array-initializer]
See ‘/data/gannet/ripley/R/packages/tests-clang/htmltidy.Rcheck/00install.out’ for details.
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data  12.1Mb
    doc    2.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
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  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
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  7.6Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   5.0Mb
Running ‘testthat.R’ [15s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(hutils)
  > 
  > test_check("hutils")
  OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
  OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  ── 1. Failure: Mutate other weighted with mass (@test_1-0-0_mutate_other.R#206) 
  uniqueN(routes_pax_othered[["dest"]]) not equal to 7.
  1/1 mismatches
  [1] 6 - 7 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 591 SKIPPED: 14 FAILED: 1
  1. Failure: Mutate other weighted with mass (@test_1-0-0_mutate_other.R#206) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘HWxtest/libs/HWxtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
File ‘hyphenatr/libs/hyphenatr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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  8.7Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.5Mb
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.
Found the following significant warnings:
  IBDsim.c:27:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:39:20: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:54:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:61:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/IBDsim.Rcheck/00install.out’ for details.
Running examples in ‘IBDsim-Ex.R’ failed
The error most likely occurred in:

> ### Name: oneLocusIBD
> ### Title: Estimating pairwise IBD coefficients
> ### Aliases: oneLocusIBD
> ### Keywords: math
> 
> ### ** Examples
> 
> ### Example 1: Full siblings
> x <- nuclearPed(2) 
> Nsim <- 100 # Should be increased substantially
> 
> # Autosomal kappa: Estimate vs exact 
> k_est = oneLocusIBD(x, ind1=3, ind2=4, Nsim=Nsim, seed=123)
---------------
Performing unconditional simulation
Mode: autosomal 
Recombination model: haldane (poisson process) 
Number of simulations: 100 
Simulation finished. Time used: 0.086 seconds
---------------
IBD analysis finished. Total time used: 0.088 seconds.
> k_exact = c(0.25, 0.5, 0.25)
> stopifnot(all(round(k_est - k_exact, 1) == 0))
Error: all(round(k_est - k_exact, 1) == 0) is not TRUE
Execution halted
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
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
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.
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    R     14.5Mb
    doc    4.8Mb
    libs  10.3Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
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.
Found the following significant warnings:
  RccpSource_.cpp:978:54: warning: explicitly assigning value of variable of type 'Rcpp::NumericVector' (aka 'Vector<14>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/icosa.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      2.3Mb
Running examples in ‘icsurvROC-Ex.R’ failed
The error most likely occurred in:

> ### Name: icsurvROC
> ### Title: Interval Censored survival ROC
> ### Aliases: icsurvROC
> ### Keywords: Semiparametric Cox proportional hazards, local NPMLE, maximum
> ###   likelihood croos validation
> 
> ### ** Examples
> 
> Time=   c(1,2,5,3,9,8,9,4,6,4)
> Status= c(1,1,1,0,1,1,1,0,0,0)
> Marker= c(8,2,6,3,1,4,5,1,3,7)
> 
> #np at year 3
> nobs=length(Time)
> span=sd(Marker)*nobs^(-1/7)
> RES1=icsurvROC(Time, Status, Marker, pred.time=3, method="np", span=span)
> print(RES1)
$tpf
 [1] 1.0000000 0.8264495 0.7402257 0.5663736 0.4751137 0.3892563 0.2863814
 [8] 0.1562429 0.0000000 0.0000000

$fpf
 [1] 1.00000000 0.78620335 0.67901738 0.46537808 0.36081908 0.25344200
 [7] 0.15494160 0.07066247 0.00000000 0.00000000

$cut.value
 [1] -Inf    1    2    3    4    5    6    7    8  Inf

$auc
[1] 0.5770804

$eval.time
[1] 3

> 
> #sp at year 3
> RES2=icsurvROC(Time, Status, Marker, pred.time=3, method="sp")
[1] "Proportional hazards model does not converge"
Error in if (St != 1) tpf.a[i] = (1 - Fc - Sct)/(1 - St) : 
  missing value where TRUE/FALSE needed
Calls: icsurvROC -> icROC
Execution halted
installed size is 72.2Mb
  sub-directories of 1Mb or more:
    libs  71.1Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘gtools’ ‘maxLik’
  All declared Imports should be used.
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  26.5Mb
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.
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.
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.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  13.7Mb
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 43.6Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       5.3Mb
    extdata   1.0Mb
    include   2.8Mb
    libs     32.4Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
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.
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.
File ‘inarmix/libs/inarmix.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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(incidence)
  > 
  > test_check("incidence")
  ── 1. Failure: construction - numeric input (@test-incidence.R#90)  ────────────
  `incidence(dat_num)` produced unexpected warnings.
  Expected match: Flooring from non-integer date caused approximations:\nMean relative difference: 0.0228833
  Actual values:
  * Flooring from non-integer date caused approximations:
  Mean relative difference: 0.02304147
  
  ── 2. Failure: Expected values, no group (@test-incidence.R#312)  ──────────────
  `res3` has changed from known value recorded in 'rds/incidence.res3.rds'.
  Component "counts": Mean relative difference: 0.3271538
  
  ── 3. Failure: Expected values, no group (@test-incidence.R#313)  ──────────────
  `res4` has changed from known value recorded in 'rds/incidence.res4.rds'.
  Component "counts": Mean relative difference: 0.9704142
  
  ── 4. Failure: Expected values, no group (@test-incidence.R#316)  ──────────────
  `res7` has changed from known value recorded in 'rds/incidence.res7.rds'.
  Component "counts": Mean relative difference: 0.172
  
  ── 5. Failure: Expected values, no group (@test-incidence.R#317)  ──────────────
  `res8` has changed from known value recorded in 'rds/incidence.res8.rds'.
  Component "counts": Mean relative difference: 0.1052632
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 218 SKIPPED: 18 FAILED: 5
  1. Failure: construction - numeric input (@test-incidence.R#90) 
  2. Failure: Expected values, no group (@test-incidence.R#312) 
  3. Failure: Expected values, no group (@test-incidence.R#313) 
  4. Failure: Expected values, no group (@test-incidence.R#316) 
  5. Failure: Expected values, no group (@test-incidence.R#317) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
Running ‘testthat.R’ [17s/44s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(infer)
  > 
  > test_check("infer")
  Setting `type = "permute"` in `generate()`.
  ── 1. Failure: conf_int argument works (@test-wrappers.R#141)  ─────────────────
  no_var_equal == var_equal isn't false.
  
  ── 2. Failure: conf_int argument works (@test-wrappers.R#153)  ─────────────────
  shortcut_no_var_equal == shortcut_var_equal isn't false.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 347 SKIPPED: 0 FAILED: 2
  1. Failure: conf_int argument works (@test-wrappers.R#141) 
  2. Failure: conf_int argument works (@test-wrappers.R#153) 
  
  Error: testthat unit tests failed
  Execution halted
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.
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.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
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 29.1Mb
  sub-directories of 1Mb or more:
    libs  28.8Mb
File ‘intervals/libs/intervals.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   7.5Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘expm’
  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  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘RcmdrPlugin.IPSUR’ ‘TeachingDemos’ ‘actuar’ ‘aplpack’
  ‘binom’ ‘boot’ ‘coin’ ‘distrEx’ ‘e1071’ ‘lmtest’ ‘mvtnorm’ ‘prob’
  ‘qcc’ ‘reshape’ ‘scatterplot3d’ ‘vcd’
  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.
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.
File ‘IsingSampler/libs/IsingSampler.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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:
    help   1.1Mb
    libs   6.3Mb
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.
File ‘Iso/libs/Iso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Namespace in Imports field not imported from: ‘comtradr’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'gurobi', 'Rcplex', 'cplexAPI'
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
File ‘JAGUAR/libs/JAGUAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(janitor)
  > 
  > test_check("janitor")
  ── 1. Failure: users can supply own Ns (@test-adorn-ns.R#129)  ─────────────────
  `%>%`(...) not equal to data.frame(...).
  Component "big": 2 string mismatches
  Component "small": 2 string mismatches
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 438 SKIPPED: 0 FAILED: 1
  1. Failure: users can supply own Ns (@test-adorn-ns.R#129) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Output from running autoconf:
  configure.ac:103: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
  ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
  ../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from...
  ../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from...
  configure.ac:103: the top level
Non-standard files/directories found at top level:
  ‘getsp.class’ ‘getsp.java’ ‘version’
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: ‘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  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   6.9Mb
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.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   4.1Mb
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.
Running ‘testthat.R’ [36s/68s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(jpmesh)
  > 
  > test_check("jpmesh")
  ── 1. Failure: Generate random meshcode (@test-rmesh.R#8)  ─────────────────────
  `res` not equal to "50304610".
  1/1 mismatches
  x[1]: "64394175"
  y[1]: "50304610"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 133 SKIPPED: 0 FAILED: 1
  1. Failure: Generate random meshcode (@test-rmesh.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
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.
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    include   1.2Mb
    libs      4.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Namespace in Imports field not imported from: ‘mclust’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(kamila)
  > 
  > test_check("kamila")
  ── 1. Failure: gmsClust runs as expected, small data set (@test_gmsClust.R#13)  
  res1$results$cluster not equal to c(1, 1, 2, 1, 1, 2, 1, 2, 2, 1, 2, 1, 2, 2, 2).
  6/15 mismatches (average diff: 1)
  [1]  2 - 1 ==  1
  [3]  1 - 2 == -1
  [6]  1 - 2 == -1
  [8]  1 - 2 == -1
  [11] 1 - 2 == -1
  [15] 1 - 2 == -1
  
  ── 2. Failure: KAMILA runs as expected, small data set (@test_kamila.R#19)  ────
  res1$finalMemb not identical to c(2, 1, 2, 1, 1, 2, 1, 1, 1, 2, 1, 1, 2, 2, 1).
  15/15 mismatches (average diff: 1)
  [1] 1 - 2 == -1
  [2] 2 - 1 ==  1
  [3] 1 - 2 == -1
  [4] 2 - 1 ==  1
  [5] 2 - 1 ==  1
  [6] 1 - 2 == -1
  [7] 2 - 1 ==  1
  [8] 2 - 1 ==  1
  [9] 2 - 1 ==  1
  ...
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2 SKIPPED: 0 FAILED: 2
  1. Failure: gmsClust runs as expected, small data set (@test_gmsClust.R#13) 
  2. Failure: KAMILA runs as expected, small data set (@test_kamila.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Namespaces in Imports field not imported from:
  ‘EQL’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   9.6Mb
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  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
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  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
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.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(kmer)
  > test_check("kmer")
  Converting to Dayhoff(6) compressed alphabet for k > 4
  Classes: AGPST, C, DENQ, FWY, HKR, ILMV── 1. Failure: object dimensions are correct (@test_distance.R#103)  ───────────
  ncol(y.mbed) not equal to 9.
  1/1 mismatches
  [1] 8 - 9 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 24 SKIPPED: 0 FAILED: 1
  1. Failure: object dimensions are correct (@test_distance.R#103) 
  
  Error: testthat unit tests failed
  Execution halted
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.
File ‘knncat/libs/knncat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.0Mb
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.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    java   6.0Mb
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.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.9Mb
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
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 16.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  14.9Mb
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  7.5Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
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  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
Namespaces in Imports field not imported from:
  ‘collections’ ‘repr’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    2.4Mb
    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 ‘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
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.
Running examples in ‘LCA-Ex.R’ failed
The error most likely occurred in:

> ### Name: LCA
> ### Title: Localised Co-dependency Analysis
> ### Aliases: LCA
> 
> ### ** Examples
> 
> ## create a data matrix
> 
> x <- array(runif(1200),dim=c(40,12))
> 
> ## implant similarity across a 'clique'
> 
> clique.cols <- sample(ncol(x),4)
> x[,clique.cols] <- x[,clique.cols] + rnorm(nrow(x))
> 
> ## scale x to (0,1)
> 
> x[x<0] <- 0
> x[x>1] <- 1
> 
> ## choose a 'seed' feature and some partner
> 
> seed.row <- sample(nrow(x),1)
> partner.row <- sample(setdiff(c(1:nrow(x)),seed.row),1)
> 
> x[c(seed.row,partner.row),clique.cols] <- x[c(seed.row,partner.row),clique.cols] + 
+ rep(rnorm(length(clique.cols)),each=2)
> 
> ## calibrate PTL models to dataset
> 
> PTL.fit <- fitPTLmodel(x,nPairs=15)
1 models successfully fitted out of 12 
Error in fitPTLmodel(x, nPairs = 15) : 
  Rerun model calibration (possibly with higher nPairs), no successful fits this time.
Execution halted
File ‘lcopula/libs/lcopula.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
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
Namespace in Imports field not imported from: ‘rgeos’
  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 ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Object: ‘leaps.o’
File ‘leaps/libs/leaps.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:
  ‘gridExtra’ ‘scales’ ‘tibble’
  All declared Imports should be used.
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.
Note: found 10 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
Output from running autoconf:
  configure.ac:17: error: possibly undefined macro: AC_DEFINE
        If this token and others are legitimate, please use m4_pattern_allow.
        See the Autoconf documentation.
  configure.ac:36: error: possibly undefined macro: AC_MSG_WARN
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.
Running examples in ‘liayson-Ex.R’ failed
The error most likely occurred in:

> ### Name: clusterCells
> ### Title: Grouping cells into clones.
> ### Aliases: clusterCells
> 
> ### ** Examples
> 
> data(cnps)
> set.seed(2)
> rcells = sample(colnames(cnps), 120)
> outc = clusterCells(cnps[apply(cnps, 1, var)>0, rcells])
[1] "Neither k nor h is set."
[1] "Using Akaike information criterion to decide number of clusters..."
Error in kmeans(t(cnps), centers = x) : 
  more cluster centers than distinct data points.
Calls: clusterCells ... sapply -> lapply -> FUN -> .kmeansAIC -> ncol -> kmeans
Execution halted
File ‘libamtrack/libs/libamtrack.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.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.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data      3.8Mb
    extdata   1.1Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘devtools’ ‘e1071’ ‘glmnet’ ‘hash’ ‘pamr’ ‘randomForest’
  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.
File ‘linkcomm/libs/linkcomm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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   5.3Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   8.9Mb
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  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs      21.9Mb
    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: ‘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.
Namespace in Imports field not imported from: ‘shinyjs’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘checkmate’
  All declared Imports should be used.
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.
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.
File ‘logconcens/libs/logconcens.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘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 ‘logitchoice/libs/logitchoice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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 24.8Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
Running ‘testthat.R’ [7s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lolR)
  > 
  > test_check("lolR")
  ── 1. Failure: Optimal Embedding Dimensions (@test-xval.R#45)  ─────────────────
  result.rs$optimal.lhat not equal to result.rs.noset$optimal.lhat.
  Lengths differ: 2 is not 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 446 SKIPPED: 0 FAILED: 1
  1. Failure: Optimal Embedding Dimensions (@test-xval.R#45) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [16s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(loo)
  This is loo version 2.0.0.
  **NOTE: As of version 2.0.0 loo defaults to 1 core but we recommend using as many as possible. Use the 'cores' argument or set options(mc.cores = NUM_CORES) for an entire session. Visit mc-stan.org/loo/news for details on other changes.
  
  Attaching package: 'loo'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  > Sys.setenv("R_TESTS" = "")
  > test_check("loo")
  ── 1. Failure: weighted quantiles work (@test_E_loo.R#155)  ────────────────────
  .wquant(x1, w1, pr) not equal to .wquant_sim(x1, w1, pr, n_sim = 2e+06).
  35/39 mismatches (average diff: 0.012)
  [1]  -2.005 - -1.987 == -0.01808
  [2]  -1.688 - -1.647 == -0.04073
  [3]  -1.472 - -1.440 == -0.03245
  [4]  -1.269 - -1.280 ==  0.01101
  [5]  -1.143 - -1.152 ==  0.00863
  [6]  -1.040 - -1.042 ==  0.00202
  [7]  -0.946 - -0.943 == -0.00287
  [8]  -0.831 - -0.837 ==  0.00630
  [10] -0.658 - -0.667 ==  0.00869
  ...
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 378 SKIPPED: 0 FAILED: 1
  1. Failure: weighted quantiles work (@test_E_loo.R#155) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘futile.options’ ‘ggfortify’ ‘grDevices’ ‘stats’
  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  5.5Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
File ‘lpSolveAPI/libs/lpSolveAPI.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 ‘lpSolve/libs/lpSolve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘ggplot2’ ‘knitr’
  All declared Imports should be used.
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
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lsbclust)
  Loading required package: ggplot2
  > 
  > test_check("lsbclust")
  K-means on overall means...	DONE
  ── 1. Failure: cluster vector (@test_orc.R#29)  ────────────────────────────────
  ovl$cluster not identical to ovltest$cluster.
  24/220 mismatches (average diff: 1.33)
  [1]    8 - 10 == -2
  [14]  10 -  9 ==  1
  [31]   9 -  8 ==  1
  [57]   9 -  8 ==  1
  [61]   8 - 10 == -2
  [64]   8 - 10 == -2
  [77]  10 -  9 ==  1
  [84]  10 -  9 ==  1
  [112]  9 -  8 ==  1
  ...
  
  ── 2. Failure: cluster means (@test_orc.R#33)  ─────────────────────────────────
  ovl$centers not equal to ovltest$centers.
  3/12 mismatches (average diff: 3.68)
  [8]  7.22 - 2.70 ==  4.52
  [9]  2.70 - 1.70 ==  1.00
  [10] 1.70 - 7.22 == -5.52
  
  K-means on row margins...	DONE
  K-means on column margins...	DONE
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 34 SKIPPED: 0 FAILED: 2
  1. Failure: cluster vector (@test_orc.R#29) 
  2. Failure: cluster means (@test_orc.R#33) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 48.2Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  46.1Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘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.
File ‘lucr/libs/lucr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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   2.1Mb
    libs   3.5Mb
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘raster’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘polspline’
  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 27.5Mb
  sub-directories of 1Mb or more:
    libs  27.1Mb
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 12.8Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs   5.7Mb
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.
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
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 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Namespaces in Imports field not imported from:
  ‘Metrics’ ‘plyr’ ‘tidyr’
  All declared Imports should be used.
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
installed size is 41.8Mb
  sub-directories of 1Mb or more:
    doc           1.2Mb
    htmlwidgets   1.5Mb
    libs         37.8Mb
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
File ‘maptpx/libs/maptpx.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘betareg’
  All declared Imports should be used.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
File ‘marqLevAlg/libs/marqLevAlg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs  10.7Mb
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  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Running ‘testthat.R’ [27s/63s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(matrixTests)
  > 
  > test_check("matrixTests")
  ── 1. Failure: monte-carlo random testing gives equal results (@test-correct-cor
  `t1` not equal to `t2`.
  Component "conf.level": Mean absolute difference: 0.2742743
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 836 SKIPPED: 0 FAILED: 1
  1. Failure: monte-carlo random testing gives equal results (@test-correct-cor_pearson.R#58) 
  
  Error: testthat unit tests failed
  Execution halted
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 13.3Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  10.9Mb
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  5.5Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
installed size is 39.8Mb
  sub-directories of 1Mb or more:
    libs  38.7Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
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.
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.
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
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.
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.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   8.4Mb
File ‘medfate/libs/medfate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘MEET/libs/MEET.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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’ ‘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’ ‘shinydashboard’
  ‘shinydashboardPlus’ ‘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  5.4Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.3Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   5.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Running examples in ‘metacart-Ex.R’ failed
The error most likely occurred in:

> ### Name: FEmrt
> ### Title: Fixed effect meta-tree
> ### Aliases: FEmrt
> 
> ### ** Examples
> 
> data(dat.BCT2009)
> FEtree <- FEmrt(g ~ T1 + T2+ T4 + T25, vi = vi, data = dat.BCT2009, c = 0.5)
Warning in FEmrt(g ~ T1 + T2 + T4 + T25, vi = vi, data = dat.BCT2009, c = 0.5) :
  no moderator effect was detected
> print(FEtree)

Fixed Effects Meta-Tree (K = 106 studies); 
FEmrt(formula = g ~ T1 + T2 + T4 + T25, data = dat.BCT2009, vi = vi, 
    c = 0.5)

No moderator effect was detected
use summary() to see the meta-analysis results> summary(FEtree)

Fixed Effects meta-tree (K = 106 studies); 
FEmrt(formula = g ~ T1 + T2 + T4 + T25, data = dat.BCT2009, vi = vi, 
    c = 0.5)

No moderator effect was detected

Test for Heterogeneity under FE assumption:
Q = 253.0357 (df = 105), p-value < 1e-04;

Fixed Effect Meta-analysis Results:
   no.      g     se   zval   pval  ci.lb  ci.ub        
   106  0.229  0.012 18.803  0.000  0.206  0.253    *** 
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 

> plot(FEtree)
Error in `rownames<-`(`*tmp*`, value = rank(as.numeric(rownames(frame)))) : 
  attempt to set 'rownames' on an object with no dimensions
Calls: plot -> plot.FEmrt -> rownames<-
Execution halted
Namespaces in Imports field not imported from:
  ‘ggrepel’ ‘reshape’ ‘svglite’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘DT’ ‘GEOmetadb’ ‘RMySQL’ ‘RSQLite’ ‘gplots’ ‘pheatmap’ ‘readr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘shiny’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
File ‘MetaSKAT/libs/MetaSKAT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 65.7Mb
  sub-directories of 1Mb or more:
    libs  65.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
Running ‘testthat.R’ [55s/55s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(metR)
  > library(vdiffr)
  > 
  > test_check("metR")
  OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
  OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  ── 1. Failure: EOF changes probs (@test_eof.R#21)  ─────────────────────────────
  {
      ...
  } not identical to 1524903.
  1/1 mismatches
  [1] 1523828 - 1524903 == -1075
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 62 SKIPPED: 16 FAILED: 1
  1. Failure: EOF changes probs (@test_eof.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  binomial-twostage.cpp:78:4: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  binomial-twostage.cpp:280:4: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/mets.Rcheck/00install.out’ for details.
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.1Mb
    libs  19.2Mb
    misc   1.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
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.
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.
Found the following significant warnings:
  mat.c:1867:9: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/mgcv.Rcheck/00install.out’ for details.
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.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mgsub)
  > 
  > test_check("mgsub")
  ── 1. Failure: multicharacter censor works (@test_mgsub_censor.R#53)  ──────────
  mgsub_censor("What the flip?", "flip", "?#!*", seed = 10) not equal to "What the !##!?".
  1/1 mismatches
  x[1]: "What the !?#*?"
  y[1]: "What the !##!?"
  
  ── 2. Failure: multicharacter censor works (@test_mgsub_censor.R#54)  ──────────
  mgsub_censor(...) not equal to "What the !##!?".
  1/1 mismatches
  x[1]: "What the !?#*?"
  y[1]: "What the !##!?"
  
  ── 3. Failure: multicharacter censor works (@test_mgsub_censor.R#55)  ──────────
  mgsub_censor("What the flip?", "flip", c("?#", "!*"), seed = 10) not equal to "What the !##!?".
  1/1 mismatches
  x[1]: "What the !?#*?"
  y[1]: "What the !##!?"
  
  ── 4. Failure: multicharacter censor can be used badly (@test_mgsub_censor.R#61)
  mgsub_censor(...) not equal to "What the !*?#?#!*?".
  1/1 mismatches
  x[1]: "What the ?#?#!*!*?"
  y[1]: "What the !*?#?#!*?"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 56 SKIPPED: 0 FAILED: 4
  1. Failure: multicharacter censor works (@test_mgsub_censor.R#53) 
  2. Failure: multicharacter censor works (@test_mgsub_censor.R#54) 
  3. Failure: multicharacter censor works (@test_mgsub_censor.R#55) 
  4. Failure: multicharacter censor can be used badly (@test_mgsub_censor.R#61) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  21.1Mb
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.
File ‘mht/libs/mht.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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:
    libs   5.1Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Running ‘testthat.R’ [74s/248s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mice)
  Loading required package: lattice
  
  Attaching package: 'mice'
  
  The following objects are masked from 'package:base':
  
      cbind, rbind
  
  > 
  > test_check("mice")
  ── 1. Failure: retains same numerical result (@test-pool.R#13)  ────────────────
  unname(getqbar(est)) not equal to `mn`.
  5/5 mismatches (average diff: 0.895)
  [1] 19.7878 - 18.7617 ==  1.02603
  [2]  0.0513 -  0.0536 == -0.00229
  [3] -6.1563 - -4.5737 == -1.58260
  [4] -7.7136 - -6.6360 == -1.07766
  [5]  2.9521 -  2.1636 ==  0.78847
  
  ── 2. Failure: retains same numerical result (@test-pool.R#14)  ────────────────
  unname(summary(est)[, "std.error"]) not equal to `se`.
  5/5 mismatches (average diff: 0.329)
  [1] 3.4259 - 4.0028 == -0.57694
  [2] 0.0187 - 0.0224 == -0.00363
  [3] 1.6195 - 2.0340 == -0.41452
  [4] 1.9746 - 2.4598 == -0.48513
  [5] 1.8642 - 2.0290 == -0.16475
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 274 SKIPPED: 0 FAILED: 2
  1. Failure: retains same numerical result (@test-pool.R#13) 
  2. Failure: retains same numerical result (@test-pool.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘microclass/libs/microclass.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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’ [27s/68s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > #library(microsamplingDesign)
  > 
  > #source("generateTestData.R")
  > 
  > #test_check("microsamplingDesign")
  > 
  > testthat::test_check("microsamplingDesign")
  Loading required package: microsamplingDesign
  start Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  2 cores── 1. Failure: Equal ranking timePoints (@testRankTimePoints.R#43)  ────────────
  rankTimePointsOrig@ranking not equal to rankedTimePointsNew@ranking.
  Component "name": 7 string mismatches
  Component "criterion": Mean relative difference: 0.04047401
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 21 SKIPPED: 3 FAILED: 1
  1. Failure: Equal ranking timePoints (@testRankTimePoints.R#43) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘MigClim/libs/MigClim.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Objects: ‘genclust.o’, ‘migrate.o’, ‘src_cell.o’, ‘validate.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Objects: ‘genclust.o’, ‘migrate.o’
File ‘MigClim/libs/MigClim.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:
  ‘FactoMineR’ ‘softImpute’
  All declared Imports should be used.
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    libs  22.8Mb
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DiceDesign’ ‘MaxPro’ ‘doSNOW’ ‘jpeg’
  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  7.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   5.8Mb
File ‘misclassGLM/libs/misclassGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
installed size is 42.7Mb
  sub-directories of 1Mb or more:
    libs  40.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
File ‘MixedDataImpute/libs/MixedDataImpute.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
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.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘foreach’
  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.
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: ‘aws.s3’
  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.
Running examples in ‘ML.MSBD-Ex.R’ failed
The error most likely occurred in:

> ### Name: likelihood_MSBD_unresolved
> ### Title: Likelihood calculation for unresolved trees
> ### Aliases: likelihood_MSBD_unresolved
> 
> ### ** Examples
> 
> # Simulate a random phylogeny
> set.seed(24)
> tree <- ape::rcoal(10)
> 
> # Calculate the log likelihood under a constant birth-death model (i.e, no shifts) 
> # with unresolved tips
> likelihood_MSBD_unresolved(tree, shifts = c(), gamma = 0, lambdas = 10, mus = 1, 
+                            lineage_counts = c(2,5,1,3,1,1,1,1,2,6), tcut = 0.05)
Error in likelihood_MSBD_unresolved(tree, shifts = c(), gamma = 0, lambdas = 10,  : 
  Invalid cut-off time for tip t7
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Using_ML.MSBD.Rmd’ using rmarkdown
Quitting from lines 57-58 (Using_ML.MSBD.Rmd) 
Error: processing vignette 'Using_ML.MSBD.Rmd' failed with diagnostics:
Tree edge 2 has negative length
--- failed re-building ‘Using_ML.MSBD.Rmd’

SUMMARY: processing the following file failed:
  ‘Using_ML.MSBD.Rmd’

Error: Vignette re-building failed.
Execution halted
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.
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    libs  28.3Mb
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    libs  21.2Mb
Output from running autoconf:
  /usr/bin/m4:configure.ac:25: cannot open `m4/ax_openmp.m4': No such file or directory
  autom4te: /usr/bin/m4 failed with exit status: 1
Namespace in Imports field not imported from: ‘plotrix’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘matlib’
  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.
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.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    1.8Mb
    libs   3.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
Running ‘testthat.R’ [64s/182s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > # Sys.setenv("MONETDBLITE_INMEMORY" = "yes")
  > # test_check("MonetDBLite")
  > Sys.setenv("MONETDBLITE_INMEMORY" = "no")
  > test_check("MonetDBLite")
  Loading required package: MonetDBLite
  ── 1. Failure: db allows svyby commands (@test_05_survey.R#60)  ────────────────
  round(...) not equal to 0.022.
  1/1 mismatches
  [1] 0.019 - 0.022 == -0.003
  
  ── 2. Failure: db allows svyby commands (@test_05_survey.R#62)  ────────────────
  ...[] not equal to 10.11.
  1/1 mismatches
  [1] 10.3 - 10.1 == 0.23
  
  [1] "E"
  [1] "H"
  [1] "M"
  ── 3. Failure: db allows svyby commands (@test_05_survey.R#66)  ────────────────
  round(SE(a)[2], 2) not equal to 4708.41.
  1/1 mismatches
  [1] 5476 - 4708 == 768
  
  ── 4. Failure: db allows svyby commands (@test_05_survey.R#67)  ────────────────
  as.numeric(round(cv(a)[2], 4)) not equal to 0.2975.
  1/1 mismatches
  [1] 0.346 - 0.297 == 0.0486
  
  ── 5. Failure: db allows svyby commands (@test_05_survey.R#69)  ────────────────
  round(confint(a, df = degf(rclus1))[2, 2], 2) not equal to 30808.26.
  1/1 mismatches
  [1] 33252 - 30808 == 2443
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 315 SKIPPED: 13 FAILED: 5
  1. Failure: db allows svyby commands (@test_05_survey.R#60) 
  2. Failure: db allows svyby commands (@test_05_survey.R#62) 
  3. Failure: db allows svyby commands (@test_05_survey.R#66) 
  4. Failure: db allows svyby commands (@test_05_survey.R#67) 
  5. Failure: db allows svyby commands (@test_05_survey.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
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.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   8.4Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.9Mb
Error(s) in re-building vignettes:
--- re-building ‘estimatingWindSpeed.Rmd’ using rmarkdown
--- finished re-building ‘estimatingWindSpeed.Rmd’

--- re-building ‘windEstimationParameters.Rmd’ using rmarkdown
Quitting from lines 92-93 (windEstimationParameters.Rmd) 
Error: processing vignette 'windEstimationParameters.Rmd' failed with diagnostics:
some 'x' not counted; maybe 'breaks' do not span range of 'x'
--- failed re-building ‘windEstimationParameters.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
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.
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 18.4Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  16.4Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
File ‘MRH/libs/MRH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 18.3Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
installed size is 48.3Mb
  sub-directories of 1Mb or more:
    libs  47.9Mb
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.
Running ‘test_base.R’ [65s/168s]
Running the tests in ‘tests/test_base.R’ failed.
Complete output:
  > library(testthat)
  > test_check("msm")
  Loading required package: msm
  ── 1. Failure: Information matrix (@test_deriv.r#138)  ─────────────────────────
  c(0.88475550512612, 0.202501688704573, -0.474183198550202) not equal to tm$paramdata$info[1:3].
  3/3 mismatches (average diff: 0.284)
  [1]  0.885 -  1.0455 == -0.161
  [2]  0.203 -  0.0872 ==  0.115
  [3] -0.474 - -1.0490 ==  0.575
  
  ── 2. Failure: piecewise constant intensities with pci, with other covariates (@
  448.1228 not equal to cav5cov.msm$minus2loglik.
  1/1 mismatches
  [1] 448 - 456 == -7.79
  
  ── 3. Failure: piecewise constant intensities with pci, with other covariates (@
  448.1228 not equal to cav5cov.msm$minus2loglik.
  1/1 mismatches
  [1] 448 - 456 == -7.79
  
  ── 4. Failure: piecewise constant intensities with pci, with uncentered covariat
  449.692 not equal to cav5cov.msm$minus2loglik.
  1/1 mismatches
  [1] 450 - 458 == -7.82
  
  ── 5. Failure: piecewise constant intensities with pci, with uncentered covariat
  449.692 not equal to cav5cov.msm$minus2loglik.
  1/1 mismatches
  [1] 450 - 458 == -7.82
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 462 SKIPPED: 2 FAILED: 5
  1. Failure: Information matrix (@test_deriv.r#138) 
  2. Failure: piecewise constant intensities with pci, with other covariates (@test_models.r#202) 
  3. Failure: piecewise constant intensities with pci, with other covariates (@test_models.r#210) 
  4. Failure: piecewise constant intensities with pci, with uncentered covariates (@test_models.r#218) 
  5. Failure: piecewise constant intensities with pci, with uncentered covariates (@test_models.r#226) 
  
  Error: testthat unit tests failed
  Execution halted
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.
File ‘multicool/libs/multicool.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 135.8Mb
  sub-directories of 1Mb or more:
    libs  135.6Mb
Namespace in Imports field not imported from: ‘igraphdata’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘webshot’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    libs  29.8Mb
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.
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  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.4Mb
Namespace in Imports field not imported from: ‘biomartr’
  All declared Imports should be used.
Running ‘testthat.R’ [67s/174s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(myTAI)
  > 
  > test_check("myTAI")
  
  
  
  ── 1. Failure: PlotEnrichment() computes correct values... (@test-PlotEnrichment
  round(...) not equal to round(c(1, 1, 0.2406024, 1, 1, 0.4215795, 1), 5).
  5/7 mismatches (average diff: 0.519)
  [1] 0.525 - 1.000 == -0.475
  [3] 0.553 - 0.241 ==  0.313
  [5] 0.350 - 1.000 == -0.650
  [6] 1.000 - 0.422 ==  0.578
  [7] 0.422 - 1.000 == -0.578
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 265 SKIPPED: 1 FAILED: 1
  1. Failure: PlotEnrichment() computes correct values... (@test-PlotEnrichment.R#271) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
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  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.0Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘stats’
  All declared Imports should be used.
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.
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.
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:
    libs   6.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.9Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.
File ‘neariso/libs/neariso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘igraph’
  All declared Imports should be used.
File ‘netcoh/libs/netcoh.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 10.6Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   6.7Mb
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  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   6.3Mb
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.
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
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.
Namespaces in Imports field not imported from:
  ‘ProjectTemplate’ ‘devtools’ ‘plyr’ ‘survival’
  All declared Imports should be used.
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    CppCode        1.1Mb
    R              5.7Mb
    classic-bugs   1.6Mb
    include        5.8Mb
    tests          1.5Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Namespaces in Imports field not imported from:
  ‘PreciseSums’ ‘numDeriv’
  All declared Imports should be used.
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.
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: ‘uroot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lwgeom’
  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.
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.
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.
File ‘norm2/libs/norm2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc   8.6Mb
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.
File ‘not/libs/not.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  ./SpecialFunctions.h:122:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./SpecialFunctions.h:153:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./SpecialFunctions.h:154:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./SpecialFunctions.h:155:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./SpecialFunctions.h:197:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./SpecialFunctions.h:198:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/data/gannet/ripley/R/packages/tests-clang/NPBayesImputeCat.Rcheck/00install.out’ for details.
Found the following significant warnings:
  utilities.c:175:32: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/npcp.Rcheck/00install.out’ for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
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 ‘npsp/libs/npsp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’ ‘tidyverse’ ‘tsibble’
  All declared Imports should be used.
installed size is 23.2Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  19.2Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
Note: found 13172 marked Latin-1 strings
installed size is 39.0Mb
  sub-directories of 1Mb or more:
    extdata  38.9Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   8.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.8Mb
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
File ‘oai/libs/oai.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.5Mb
    test_files   4.2Mb
File ‘OceanView/libs/OceanView.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.5Mb
    help   2.4Mb
    libs   3.4Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 101.5Mb
  sub-directories of 1Mb or more:
    libs  101.0Mb
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.
File ‘onlinePCA/libs/onlinePCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   4.8Mb
installed size is 202.1Mb
  sub-directories of 1Mb or more:
    R         2.5Mb
    libs    191.9Mb
    models    4.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
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.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.3Mb
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  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Running ‘anova.R’
  Running ‘clm.fit.R’
  Running ‘clm.formula.R’
  Running ‘clmm.R’ [10s/11s]
  Running ‘clmm.control.R’
  Running ‘clmm.formula.R’
  Running ‘confint.R’
  Running ‘nominal.test.R’
  Running ‘test-all.R’ [28s/32s]
  Running ‘test.clm.Theta.R’
  Running ‘test.clm.convergence.R’
  Running ‘test.clm.flex.link.R’
  Running ‘test.clm.model.matrix.R’
  Running ‘test.clm.predict.R’
  Running ‘test.clm.profile.R’
  Running ‘test.clm.single.anova.R’
  Running ‘test.general.R’
  Running ‘test.makeThresholds.R’
  Running ‘test.sign.R’
  Running ‘test0weights.R’
  Running ‘testAnova.clm2.R’
  Running ‘testCLM.R’
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > 
  > if(require(testthat) && require(ordinal)) {
  +     test_check("ordinal")
  + }
  Loading required package: testthat
  Loading required package: ordinal
  ── 1. Failure: clm gives contrast warnings when it should (@test-contrasts.R#11)
  givesWarnings(...) isn't false.
  
  ── 2. Failure: clm gives contrast warnings when it should (@test-contrasts.R#15)
  givesWarnings(...) isn't false.
  
  ── 3. Failure: clm gives contrast warnings when it should (@test-contrasts.R#19)
  givesWarnings(...) isn't false.
  
  ── 4. Failure: clm gives contrast warnings when it should (@test-contrasts.R#23)
  givesWarnings(...) isn't false.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 80 SKIPPED: 0 FAILED: 4
  1. Failure: clm gives contrast warnings when it should (@test-contrasts.R#11) 
  2. Failure: clm gives contrast warnings when it should (@test-contrasts.R#15) 
  3. Failure: clm gives contrast warnings when it should (@test-contrasts.R#19) 
  4. Failure: clm gives contrast warnings when it should (@test-contrasts.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [36s/158s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(origami)
  origami: Generalized Cross-Validation Framework
  Version: 1.0.0
  > library(data.table)
  > test_check("origami")
  OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
  OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  ── 1. Failure: CV MSE matches previous value (@test-overall.R#36)  ─────────────
  `cv_MSE` not equal to 13.32.
  1/1 mismatches
  [1] 14.1 - 13.3 == 0.791
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 34 SKIPPED: 0 FAILED: 1
  1. Failure: CV MSE matches previous value (@test-overall.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
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:
    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 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
Found the following significant warnings:
  ccaRevolution.c:31:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:44:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:97:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:98:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:110:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:111:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/osc.Rcheck/00install.out’ for details.
File ‘osc/libs/osc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   6.7Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
installed size is 33.0Mb
  sub-directories of 1Mb or more:
    libs  32.8Mb
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  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   2.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Running ‘testthat_chi2.R’ [6s/24s]
  Running ‘testthat_extractSubTree.R’ [25s/89s]
  Running ‘testthat_pacotestRegressionTests.R’ [8s/27s]
  Running ‘testthat_pacotestRvineSeqRegressionTests.R’ [66s/244s]
  Running ‘testthat_pacotestRvineSingleCopulaRegressionTests.R’ [4m/14m]
Running the tests in ‘tests/testthat_pacotestRvineSeqRegressionTests.R’ failed.
Complete output:
  > 
  > library("testthat")
  > library("pacotest")
  > 
  > test_check("pacotest", filter = "pacotestRvineSeqRegressionTests")
  ── 1. Failure: pacotestRvineSeq7 (@test-pacotestRvineSeqRegressionTests.R#194)  
  resPacotestComputed[iTest, 1:3] not equal to hardCodedResPacotestRvineSeq[iTest, 1:3].
  1/3 mismatches
  [2] 0.768 - 0.755 == 0.013
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 4 SKIPPED: 5 FAILED: 1
  1. Failure: pacotestRvineSeq7 (@test-pacotestRvineSeqRegressionTests.R#194) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [9s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(padr)
  > 
  > test_check("padr")
  ── 1. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#
  fill_by_function(x_df, y1)$y1 %>% median not equal to 14.77.
  1/1 mismatches
  [1] 14.8 - 14.8 == 0.04
  
  ── 2. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#
  fill_by_function(x_df, y1, y2)$y1 %>% median not equal to 14.77.
  1/1 mismatches
  [1] 14.8 - 14.8 == 0.04
  
  ── 3. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#
  fill_by_function(x_df, y1, y2)$y2 %>% median not equal to 22.765.
  1/1 mismatches
  [1] 25.3 - 22.8 == 2.5
  
  ── 4. Failure: fill_by_prevalent gives expected outcomes (@test_fill_functions.R
  `fill_by_prevalent(x_df, y1)` did not throw an error.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 584 SKIPPED: 1 FAILED: 4
  1. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#36) 
  2. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#37) 
  3. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#38) 
  4. Failure: fill_by_prevalent gives expected outcomes (@test_fill_functions.R#48) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data        1.6Mb
    localdata   3.1Mb
Running ‘testthat.R’ [13s/33s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(palasso)
  > 
  > testthat::test_check("palasso")
  ── 1. Failure: deviance stats (@test.R#146)  ───────────────────────────────────
  `x` isn't true.
  
  ── 2. Error: coef stats (@test.R#126)  ─────────────────────────────────────────
  attempt to select less than one element in get1index
  1: coef(fit, model = "standard_xz", s = 0) at testthat/test.R:126
  2: coef.palasso(fit, model = "standard_xz", s = 0)
  3: subset.palasso(x = object, model = model, max = max)
  
  ── 3. Error: deviance stats (@test.R#142)  ─────────────────────────────────────
  attempt to select less than one element in get1index
  1: deviance(fit, model = "standard_xz") at testthat/test.R:142
  2: deviance.palasso(fit, model = "standard_xz")
  3: subset.palasso(x = object, model = model, max = max)
  
  ── 4. Error: logLik stats (@test.R#150)  ───────────────────────────────────────
  attempt to select less than one element in get1index
  1: logLik(fit, model = "standard_xz") at testthat/test.R:150
  2: logLik.palasso(fit, model = "standard_xz")
  3: subset.palasso(x = object, model = model, max = max)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2107 SKIPPED: 2 FAILED: 4
  1. Failure: deviance stats (@test.R#146) 
  2. Error: coef stats (@test.R#126) 
  3. Error: deviance stats (@test.R#142) 
  4. Error: logLik stats (@test.R#150) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘jcolors’ ‘oompaBase’ ‘palr’ ‘pals’ ‘viridisLite’
  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.
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.
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.
Namespace in Imports field not imported from: ‘tools’
  All declared Imports should be used.
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 13.7Mb
  sub-directories of 1Mb or more:
    data      2.6Mb
    doc       1.3Mb
    extdata   9.5Mb
Namespace in Imports field not imported from: ‘AnnotationDbi’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘glue’ ‘logging’ ‘purrr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘AGread’
  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 ‘pbdDEMO/libs/pbdDEMO.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Output from running autoconf:
  configure.ac:19: error: possibly undefined macro: AC_PATH_NETCDF
        If this token and others are legitimate, please use m4_pattern_allow.
        See the Autoconf documentation.
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  9.8Mb
  sub-directories of 1Mb or more:
    lib   9.4Mb
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.
File ‘PBSddesolve/libs/PBSddesolve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.3Mb
installed size is  5.2Mb
  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  8.2Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   2.7Mb
    libs      2.8Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pander’
  All declared Imports should be used.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.1Mb
    libs   7.1Mb
Running examples in ‘pcalg-Ex.R’ failed
The error most likely occurred in:

> ### Name: backdoor
> ### Title: Find Set Satisfying the Generalized Backdoor Criterion (GBC)
> ### Aliases: backdoor
> ### Keywords: multivariate models graphs
> 
> ### ** Examples
> 
> #####################################################################
> ##DAG
> #####################################################################
> ## Simulate the true DAG
> set.seed(123)
> p <- 7
> myDAG <- randomDAG(p, prob = 0.2) ## true DAG
> 
> ## Extract the adjacency matrix of the true DAG
> true.amat <- (amat <- as(myDAG, "matrix")) != 0 # TRUE/FALSE <==> 1/0
> print.table(1*true.amat, zero.=".") # "visualization"
  1 2 3 4 5 6 7
1 . . . 1 . . .
2 . . . 1 . . 1
3 . . . . . . 1
4 . . . . 1 . .
5 . . . . . . 1
6 . . . . . . .
7 . . . . . . .
> 
> ## Compute set satisfying the GBC:
> backdoor(true.amat, 5, 7, type="dag")
[1] 4
> ## Don't show: 
> stopifnot(backdoor(true.amat, 5, 7, type="dag") == 3)
Error: backdoor(true.amat, 5, 7, type = "dag") == 3 is not TRUE
Execution halted
File ‘pcaPA/libs/pcaPA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
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.
File ‘PCIT/libs/PCIT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘caret’
  All declared Imports should be used.
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 ‘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  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Found the following significant warnings:
  spectrum.c:707:14: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:715:20: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1606:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:63: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/Peaks.Rcheck/00install.out’ for details.
File ‘Peaks/libs/Peaks.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
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.
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > ## Test `permute` using the `testthat` package
  > 
  > ## Setup
  > library("testthat")
  > library("permute")
  > 
  > ## Runs the tests in inst/tests
  > test_check("permute")
  ── 1. Failure: shuffle() works for non-contigous blocks of samples (@test-shuffl
  `x` not identical to `expected`.
  10/20 mismatches (average diff: 3)
  [3]   4 -  1 ==  3
  [4]   1 -  4 == -3
  [7]   8 -  5 ==  3
  [8]   5 -  8 == -3
  [11] 12 -  9 ==  3
  [12]  9 - 12 == -3
  [15] 16 - 13 ==  3
  [16] 13 - 16 == -3
  [19] 20 - 17 ==  3
  ...
  
  ── 2. Failure: shuffle() works for non-contigous blocks of samples (@test-shuffl
  `x` not identical to `expected`.
  10 string mismatches
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 298 SKIPPED: 0 FAILED: 2
  1. Failure: shuffle() works for non-contigous blocks of samples (@test-shuffle.R#40) 
  2. Failure: shuffle() works for non-contigous blocks of samples (@test-shuffle.R#42) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
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.
Running ‘testthat.R’ [14s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > suppressPackageStartupMessages(library(phangorn))
  > 
  > test_check("phangorn")
  loglik: -11409.87 --> -11409.87 
  ── 1. Failure: SPR distance (@test_treedist.R#100)  ────────────────────────────
  SPR.dist(tree1, trees) not equal to 1:5.
  1/5 mismatches
  [2] 1 - 2 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 120 SKIPPED: 28 FAILED: 1
  1. Failure: SPR distance (@test_treedist.R#100) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  LJMA_arms.c:297:11: warning: comparison of array 'env->p' equal to a null pointer is always false [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/PhaseType.Rcheck/00install.out’ for details.
File ‘PhaseType/libs/PhaseType.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘LJMA_arms.o’
File ‘PhaseType/libs/PhaseType.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 46.6Mb
  sub-directories of 1Mb or more:
    libs  45.9Mb
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  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
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  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
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 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
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.
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘lubridate’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   2.0Mb
    doc    3.0Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘stringi’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘XML’ ‘curl’ ‘readr’ ‘stringdist’
  All declared Imports should be used.
Running examples in ‘PkgsFromFiles-Ex.R’ failed
The error most likely occurred in:

> ### Name: pff_check_install_pkgs
> ### Title: Checks and installs a single package
> ### Aliases: pff_check_install_pkgs
> 
> ### ** Examples
> 
> pff_check_install_pkgs('dplyr')

Installing dplyrError in pkg.in %in% my.available.packages : 
  argument "my.available.packages" is missing, with no default
Calls: pff_check_install_pkgs -> %in%
Execution halted
installed size is 30.9Mb
  sub-directories of 1Mb or more:
    libs  30.8Mb
File ‘plac/libs/plac.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Namespaces in Imports field not imported from:
  ‘V8’ ‘devtools’ ‘formatR’ ‘gdata’ ‘rhandsontable’ ‘shinythemes’
  ‘sqldf’
  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.
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:
  ‘ggplot2’ ‘mixtools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.2Mb
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 ‘plyr/libs/plyr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   2.2Mb
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.
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.
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.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘tidyr’
  All declared Imports should be used.
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 10.1Mb
  sub-directories of 1Mb or more:
    R      6.9Mb
    data   2.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Running ‘test-all.R’ [15s/16s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > options(poppr.debug = TRUE)
  > test_check("poppr")
  Loading required package: poppr
  Loading required package: adegenet
  Loading required package: ade4
  
     /// adegenet 2.1.1 is loaded ////////////
  
     > overview: '?adegenet'
     > tutorials/doc/questions: 'adegenetWeb()' 
     > bug reports/feature requests: adegenetIssues()
  
  
  This is poppr version 2.8.1. To get started, type package?poppr
  OMP parallel support: available
  ── 1. Failure: rrmlg produces the correct mlgs (@test-round-robin.R#24)  ───────
  `rrx_m` not equivalent to `mlg_truth`.
  11/15 mismatches (average diff: 1.73)
  [2]  3 - 2 ==  1
  [3]  2 - 3 == -1
  [5]  4 - 1 ==  3
  [6]  1 - 2 == -1
  [7]  3 - 4 == -1
  [9]  1 - 3 == -2
  [10] 4 - 1 ==  3
  [12] 4 - 3 ==  1
  [13] 3 - 2 ==  1
  ...
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 308 SKIPPED: 186 FAILED: 1
  1. Failure: rrmlg produces the correct mlgs (@test-round-robin.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘pop.wolf/libs/pop.wolf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
File ‘POT/libs/POT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespace in Imports field not imported from: ‘shinyWidgets’
  All declared Imports should be used.
Found the following significant warnings:
  powell.c:700:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  powell.c:724:12: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/powell.Rcheck/00install.out’ for details.
File ‘powell/libs/powell.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
    Object: ‘powell.o’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘powell.o’
File ‘powell/libs/powell.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘intro_pfit.Rmd’ using rmarkdown
PP package calling ...
Follow this project on github: https://github.com/manuelreif/PP.git
Quitting from lines 131-155 (intro_pfit.Rmd) 
Error: processing vignette 'intro_pfit.Rmd' failed with diagnostics:
'x' contains missing values
--- failed re-building ‘intro_pfit.Rmd’

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

--- re-building ‘ppass_par_and_fit.Rmd’ using rmarkdown
OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
--- finished re-building ‘ppass_par_and_fit.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
File ‘PPtree/libs/PPtree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  ./shared.h:67:9: warning: result of comparison of constant 2147483648 with expression of type 'int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/praznik.Rcheck/00install.out’ for details.
File ‘prclust/libs/prclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘TH.data’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘ROCR’ ‘ada’ ‘colourpicker’ ‘corrplot’ ‘e1071’ ‘flexdashboard’
  ‘kknn’ ‘neuralnet’ ‘randomForest’ ‘rattle’ ‘rpart’ ‘scatterplot3d’
  ‘shinyAce’ ‘shinyWidgets’ ‘shinydashboardPlus’ ‘shinyjs’ ‘tidyverse’
  ‘xgboost’ ‘zip’
  All declared Imports should be used.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
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.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(probably)
  
  Attaching package: 'probably'
  
  The following objects are masked from 'package:base':
  
      as.factor, as.ordered
  
  > 
  > test_check("probably")
  ── 1. Failure: class_pred printing (@test-class-pred.R#408)  ───────────────────
  `cat_levels\(cp\)` does not match "10 Levels: dkkjddgmgwbludofdtxj grkuclzxxedqirieucmn \\.\\.\\. xsqzrsophdzxruamtfig".
  Actual value: "10 Levels: dahtypxvkpthcdtlvqjt hzgjisdnqkgulojmgiij \.\.\. zptfkhvvgpqvrqbdmevs"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 116 SKIPPED: 0 FAILED: 1
  1. Failure: class_pred printing (@test-class-pred.R#408) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
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.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc           6.5Mb
    help          2.1Mb
    htmlwidgets   2.5Mb
Namespaces in Imports field not imported from:
  ‘clipr’ ‘desc’ ‘devtools’
  All declared Imports should be used.
File ‘profdpm/libs/profdpm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    extdata   6.4Mb
    libs      2.7Mb
Package suggested but not available for checking: ‘qtbase’
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.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   2.7Mb
File ‘prospectr/libs/prospectr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Files which contain pragma(s) suppressing diagnostics:
  ‘src/geobuf.pb.h’ ‘src/rexp.pb.h’
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  6.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.2Mb
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.
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
File ‘psd/libs/psd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > #
  > # The Hadley-verse is an amazing place: unit testing via testthat
  > # See also  http://r-pkgs.had.co.nz/tests.html
  > #
  > library(testthat)
  > options(testthat.use_colours = FALSE)
  > test_check("psd")
  Loading required package: psd
  Loaded psd (1.0.1) -- Adaptive multitaper spectrum estimation
  ── 1. Failure: fftw::FFT expects numeric or complex (@test-fft.R#26)  ──────────
  `FFT(x.)` did not throw an error.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 161 SKIPPED: 0 FAILED: 1
  1. Failure: fftw::FFT expects numeric or complex (@test-fft.R#26) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘forecast’ ‘knitr’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
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  6.4Mb
  sub-directories of 1Mb or more:
    R     1.7Mb
    doc   2.4Mb
Running examples in ‘psymonitor-Ex.R’ failed
The error most likely occurred in:

> ### Name: disp
> ### Title: Generate a table with identified bubble/crisis periods
> ### Aliases: disp
> 
> ### ** Examples
> 
> data(spread)
> 
> y        <- spread$value[150:200]
> obs      <- length(y)
> swindow0 <- floor(obs*(0.01 + 1.8/sqrt(obs)))
> dim      <- obs - swindow0 + 1
> Tb       <- 24 + swindow0 - 1
> 
> # Estimate PSY statistics and CVs
> bsadf          <- PSY(y, swindow0)
> quantilesBsadf <- cvPSYwmboot(y, swindow0, Tb=Tb, nboot = 49, nCores = 2)
> quantile95     <- quantilesBsadf %*% matrix(1, nrow = 1, ncol = dim)
> 
> # locate bubble/crisis dates
> ind95        <- (bsadf > t(quantile95[2, ])) * 1
> monitorDates <- spread$date[swindow0:obs]
> OT           <- locate(ind95, monitorDates)
Warning: No bubble or crisis periods found
> 
> # Show bubble/crisis periods
> disp(OT, obs)
Error: No bubble or crisis periods found.
Execution halted
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  8.0Mb
  sub-directories of 1Mb or more:
    doc        4.6Mb
    examples   2.5Mb
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘desctable’ ‘effects’ ‘knitr’ ‘latex2exp’ ‘lme4’ ‘nlme’
  ‘nnet’ ‘ordinal’ ‘pander’ ‘papeR’
  All declared Imports should be used.
installed size is 39.4Mb
  sub-directories of 1Mb or more:
    libs  38.9Mb
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.
Namespace in Imports field not imported from: ‘FSA’
  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  5.0Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
Found the following significant warnings:
  upwindorderedv4.c:542:54: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  upwindorderedv4.c:542:72: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/QPot.Rcheck/00install.out’ for details.
File ‘QPot/libs/QPot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
File ‘QPot/libs/upwindorderedv4.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘purrr’ ‘rmarkdown’
  All declared Imports should be used.
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 12.0Mb
  sub-directories of 1Mb or more:
    data  11.8Mb
File ‘QRM/libs/QRM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.8Mb
    doc       3.0Mb
    libs      1.5Mb
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  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   1.3Mb
    libs  16.9Mb
File ‘quantreg/libs/quantreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   5.1Mb
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.
Running ‘testthat.R’ [6s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(qwraps2)
  > 
  > test_check("qwraps2")
  ── 1. Failure: Boot Strap (@test-confusion_matrix.R#15)  ───────────────────────
  round(con_mat_boot$stats[, "Boot Est"], 3) not equivalent to c(0.573, 0.669, 0.532, 0.382, 0.788).
  5/5 mismatches (average diff: 0.003)
  [1] 0.570 - 0.573 == -0.003
  [2] 0.670 - 0.669 ==  0.001
  [3] 0.527 - 0.532 == -0.005
  [4] 0.377 - 0.382 == -0.005
  [5] 0.789 - 0.788 ==  0.001
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 49 SKIPPED: 0 FAILED: 1
  1. Failure: Boot Strap (@test-confusion_matrix.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lmerTest’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin      2.9Mb
File ‘R4dfp/libs/R4dfp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘scran’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    3.6Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/race.Rcheck/00install.out’ for details.
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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Running ‘testthat.R’ [15s/38s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rags2ridges)
  > 
  > test_check("rags2ridges")
  ── 1. Failure: armaRidgeP.fused agrees with the old R implmentation (@test-armaR
  isTRUE(...) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 3893 SKIPPED: 0 FAILED: 1
  1. Failure: armaRidgeP.fused agrees with the old R implmentation (@test-armaRidgeP.fused.R#149) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
File ‘RAHRS/libs/RAHRS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    api           3.2Mb
    htmlwidgets   9.3Mb
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘stringi’
  All declared Imports should be used.
File ‘ramsvm/libs/ramsvm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.2Mb
    libs   5.0Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘dtplyr’
  All declared Imports should be used.
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.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Running ‘testthat.R’ [35s/111s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ranger)
  > 
  > test_check("ranger")
  ── 1. Failure: standard error is larger for fewer trees, probability (@test_jack
  mean(pred50$se) is not strictly less than mean(pred5$se). Difference: 0.0332
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 548 SKIPPED: 9 FAILED: 1
  1. Failure: standard error is larger for fewer trees, probability (@test_jackknife.R#160) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘Rankcluster/libs/Rankcluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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  6.3Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
File ‘RArcInfo/libs/RArcInfo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 10.2Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs   6.1Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    etc    1.9Mb
    po     1.2Mb
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
installed size is 32.1Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  29.5Mb
Error(s) in re-building vignettes:
--- re-building ‘PoS_codata.Rmd’ using rmarkdown
--- finished re-building ‘PoS_codata.Rmd’

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

--- re-building ‘customizing_plots.Rmd’ using rmarkdown
Loading required package: Rcpp
This is RBesT version 1.3.7
This is bayesplot version 1.6.0
- Online documentation and vignettes at mc-stan.org/bayesplot
- bayesplot theme set to bayesplot::theme_default()
   * Does _not_ affect other ggplot2 plots
   * See ?bayesplot_theme_set for details on theme setting
Final MCMC sample equivalent to less than 1000 independent draws.
Please consider increasing the MCMC simulation size.
--- finished re-building ‘customizing_plots.Rmd’

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

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

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

--- re-building ‘variances_MAP.Rmd’ using rmarkdown
Quitting from lines 137-148 (variances_MAP.Rmd) 
Error: processing vignette 'variances_MAP.Rmd' failed with diagnostics:
dims [product 2] do not match the length of object [3]
--- failed re-building ‘variances_MAP.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘rBeta2009/libs/rBeta2009.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    blp    7.1Mb
    libs   7.2Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Running examples in ‘rbtc-Ex.R’ failed
The error most likely occurred in:

> ### Name: Wif2PrivKey
> ### Title: Create private key from WIF
> ### Aliases: Wif2PrivKey
> 
> ### ** Examples
> 
> pk1 <- createPrivateKey()
Warning in createPrivateKey() :
  
For exemplary purposes, only.
Use at your own risk!

> wif <- PrivKey2Wif(pk1)
Warning in PrivKey2Wif(pk1) :
  
For exemplary purposes, only.
Use at your own risk!

Warning in base58CheckEncode(privkeyextcs) :
  out-of-range values treated as 0 in coercion to raw
> pk2 <- Wif2PrivKey(wif)
Warning in Wif2PrivKey(wif) :
  
For exemplary purposes, only.
Use at your own risk!

Error in Wif2PrivKey(wif) : First character in WIF does neither
correspond to mainnet nor testnet.
Execution halted
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.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rcartocolor)
  > 
  > test_check("rcartocolor")
  ── 1. Failure: palette display (@test-display.R#4)  ────────────────────────────
  `display_carto_all(n = NULL)` produced warnings.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 27 SKIPPED: 4 FAILED: 1
  1. Failure: palette display (@test-display.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
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 23.4Mb
  sub-directories of 1Mb or more:
    cont  23.3Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.0Mb
    po    2.2Mb
Running examples in ‘rcongresso-Ex.R’ failed
The error most likely occurred in:

> ### Name: fetch_despesas_deputado
> ### Title: Fetches expenditures from deputy
> ### Aliases: fetch_despesas_deputado
> 
> ### ** Examples
> 
> gastos_abel_mesquita <- fetch_despesas_deputado(id = 178957)
Error: Falha na requisicao a API dos Dados Abertos. Erro 400 ao tentar acessar: https://dadosabertos.camara.leg.br/api/v2/deputados/178957/despesas?id=178957
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rcongresso)
  > 
  > test_check("rcongresso")
  ── 1. Error: (unknown) (@test_deputados.R#81)  ─────────────────────────────────
  argument "message" is missing, with no default
  1: skip() at testthat/test_deputados.R:81
  2: structure(list(message = message), class = c("skip", "condition"))
  
  ── 2. Error: (unknown) (@test_proposicoes.R#91)  ───────────────────────────────
  could not find function "FUN1"
  1: check_api() at testthat/test_proposicoes.R:91
  2: tryCatch(setup(), error = function(e) {
         message(e)
         return(FALSE)
     }) at testthat/test_proposicoes.R:15
  3: tryCatchList(expr, classes, parentenv, handlers)
  4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5: value[[3L]](cond)
  6: message(e) at testthat/test_proposicoes.R:16
  7: withRestarts({
         signalCondition(cond)
         defaultHandler(cond)
     }, muffleMessage = function() NULL)
  8: withOneRestart(expr, restarts[[1L]])
  9: doWithOneRestart(return(expr), restart)
  
  ── 3. Error: (unknown) (@test_votacoes.R#70)  ──────────────────────────────────
  argument "message" is missing, with no default
  1: skip() at testthat/test_votacoes.R:70
  2: structure(list(message = message), class = c("skip", "condition"))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 13 SKIPPED: 0 FAILED: 3
  1. Error: (unknown) (@test_deputados.R#81) 
  2. Error: (unknown) (@test_proposicoes.R#91) 
  3. Error: (unknown) (@test_votacoes.R#70) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘introducao-rcongresso.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

Quitting from lines 36-38 (introducao-rcongresso.Rmd) 
Error: processing vignette 'introducao-rcongresso.Rmd' failed with diagnostics:
could not find function "FUN1"
--- failed re-building ‘introducao-rcongresso.Rmd’

--- re-building ‘utilizando-fetch-proposicao.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

Quitting from lines 57-63 (utilizando-fetch-proposicao.Rmd) 
Error: processing vignette 'utilizando-fetch-proposicao.Rmd' failed with diagnostics:
could not find function "FUN1"
--- failed re-building ‘utilizando-fetch-proposicao.Rmd’

SUMMARY: processing the following files failed:
  ‘introducao-rcongresso.Rmd’ ‘utilizando-fetch-proposicao.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    corpora   7.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    include   5.5Mb
    libs      1.5Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
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.
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 34.7Mb
  sub-directories of 1Mb or more:
    include   7.9Mb
    libs     26.1Mb
File ‘RcppExamples/libs/RcppExamples.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 57.1Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib      42.6Mb
    libs     12.3Mb
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 10.2Mb
  sub-directories of 1Mb or more:
    include   7.0Mb
    libs      2.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib       3.5Mb
installed size is 23.2Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
    libs     14.2Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    include   6.4Mb
    libs      4.3Mb
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:
    libs   6.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
File ‘RcppXts/libs/RcppXts.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘smcure’
  All declared Imports should be used.
File ‘rDEA/libs/rDEA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
Found the following significant warnings:
  dist.cpp:19:33: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
  dist.cpp:65:33: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
  dist.cpp:111:36: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
See ‘/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
Namespace in Imports field not imported from: ‘digest’
  All declared Imports should be used.
File ‘Rdsdp/libs/Rdsdp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gtools’
  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.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.9Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   9.0Mb
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.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
Note: found 1 marked Latin-1 string
  Note: found 1 marked UTF-8 string
  Note: found 7 strings marked as "bytes"
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
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  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   3.0Mb
Namespace in Imports field not imported from: ‘RcppRoll’
  All declared Imports should be used.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
File ‘RecordLinkage/libs/RecordLinkage.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘readr’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   4.8Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  17.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.1Mb
Namespaces in Imports field not imported from:
  ‘rlang’ ‘spatstat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘nnet’ ‘purrr’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(reinforcelearn)
  > 
  > test_check("reinforcelearn")
  ── 1. Failure: getReplayMemory returns list (@test_accessor_functions.R#22)  ───
  getReplayMemory(agent) not equal to list(...).
  Component 1: Component 2: Mean absolute difference: 1
  Component 1: Component 4: Mean relative difference: 0.03333333
  Component 2: Component 1: Mean relative difference: 0.03333333
  Component 2: Component 4: Mean relative difference: 0.05
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 20 SKIPPED: 0 FAILED: 1
  1. Failure: getReplayMemory returns list (@test_accessor_functions.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
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.
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 22.2Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
Error(s) in re-building vignettes:
--- re-building ‘rentrez_tutorial.Rmd’ using rmarkdown
Quitting from lines 296-299 (rentrez_tutorial.Rmd) 
Error: processing vignette 'rentrez_tutorial.Rmd' failed with diagnostics:
Error in the HTTP2 framing layer
--- failed re-building ‘rentrez_tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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 12.2Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
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.
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.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
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.
Namespace in Imports field not imported from: ‘segmented’
  All declared Imports should be used.
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.
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.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘stringdist’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘bitops’
  All declared Imports should be used.
installed size is 49.4Mb
  sub-directories of 1Mb or more:
    libs  48.2Mb
File ‘RFgroove/libs/RFgroove.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.3Mb
File ‘rgcvpack/libs/rgcvpack.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.7Mb
File ‘rgexf/libs/rgexf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    fonts   1.5Mb
    libs    2.7Mb
File ‘Rgnuplot/libs/Rgnuplot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking: 'playwith', 'pmg'
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extra   9.4Mb
File ‘RGtk2Extras/libs/RGtk2Extras.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 24.5Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.5Mb
    libs   8.4Mb
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
Found the following significant warnings:
  filterhr.c:21:11: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:53: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:95: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/RHRV.Rcheck/00install.out’ for details.
File ‘RHRV/libs/RHRV.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Namespace in Imports field not imported from: ‘gWidgetsRGtk2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
File ‘RInside/libs/RInside.so’:
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLdo1’, ‘R_ReplDLLinit’,
    ‘R_RunExitFinalizers’, ‘R_SetParams’, ‘R_SignalHandlers’,
    ‘R_TempDir’, ‘Rf_endEmbeddedR’, ‘Rf_initEmbeddedR’
File ‘RInside/libs/RInside.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Rip46/libs/Rip46.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
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.
Namespaces in Imports field not imported from:
  ‘gtools’ ‘knitr’ ‘usethis’
  All declared Imports should be used.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
File ‘rivr/libs/rivr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘coda’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘RcppProgress’ ‘magrittr’
  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  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  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
File ‘rlecuyer/libs/rlecuyer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 58.0Mb
  sub-directories of 1Mb or more:
    libs  57.5Mb
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
File ‘rlm/libs/rlm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

> ### Name: ggplot.magic
> ### Title: Convert a MAGIC object to a data.frame for ggplot
> ### Aliases: ggplot.magic
> 
> ### ** Examples
> 
> if (reticulate::py_module_available("magic") && require(ggplot2)) {
+ 
+ data(magic_testdata)
+ data_magic <- magic(magic_testdata, genes=c("VIM", "CDH1", "ZEB1"))
+ ggplot(data_magic, aes(VIM, CDH1, colour=ZEB1)) +
+   geom_point()
+ 
+ }
Loading required package: ggplot2
Error in py_get_attr_impl(x, name, silent) : 
  AttributeError: 'module' object has no attribute 'MAGIC'
Calls: magic ... py_get_attr_or_item -> py_get_attr -> py_get_attr_impl
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    rmd   8.3Mb
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  18.4Mb
Namespaces in Imports field not imported from:
  ‘blogdown’ ‘bookdown’ ‘bookdownplus’ ‘citr’ ‘pagedown’ ‘rticles’
  ‘tinytex’ ‘xaringan’
  All declared Imports should be used.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   5.9Mb
installed size is 42.0Mb
  sub-directories of 1Mb or more:
    libs  41.1Mb
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.
Running examples in ‘rms-Ex.R’ failed
The error most likely occurred in:

> ### Name: Function
> ### Title: Compose an S Function to Compute X beta from a Fit
> ### Aliases: Function.rms Function.cph sascode perlcode
> ### Keywords: regression methods interface models survival math
> 
> ### ** Examples
> 
> set.seed(1331)
> x1 <- exp(rnorm(100))
> x2 <- factor(sample(c('a','b'),100,rep=TRUE))
> dd <- datadist(x1, x2)
> options(datadist='dd')
> y  <- log(x1)^2+log(x1)*(x2=='b')+rnorm(100)/4
> f  <- ols(y ~ pol(log(x1),2)*x2)
> f$coef
   Intercept           x1         x1^2         x2=b    x1 * x2=b  x1^2 * x2=b 
-0.001885864 -0.019198566  1.017432226  0.047810769  1.037259829 -0.032005994 
> g  <- Function(f, digits=5)
> g
function (x1 = 1.0906, x2 = "b") 
{
    x1 <- log(x1)
    -0.0018859 - 0.019199 * x1 + 1.0174 * x1^2 + 0.047811 * (x2 == 
        "b") + (x2 == "b") * (1.0373 * x1 - 0.032006 * x1^2)
}
<environment: 0xb1eed68>
> sascode(g)
    x1 = log(x1)
    -0.0018859 - 0.019199 * x1 + 1.0174 * x1**2 + 0.047811 * (x2 = 
        "b") + (x2 = "b") * (1.0373 * x1 - 0.032006 * x1**2);
> cat(perlcode(g), '\n')
Error in expr[[3]] : subscript out of bounds
Calls: cat ... convert -> f -> paste -> convert -> f -> paste -> convert
Execution halted
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    libs  26.5Mb
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.
Error(s) in re-building vignettes:
--- re-building ‘RNewsflow.Rmd’ using rmarkdown
Quitting from lines 86-95 (RNewsflow.Rmd) 
Error: processing vignette 'RNewsflow.Rmd' failed with diagnostics:
there is no package called 'RTextTools'
--- failed re-building ‘RNewsflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rngtools)
  Loading required package: pkgmaker
  Loading required package: registry
  
  Attaching package: 'pkgmaker'
  
  The following object is masked from 'package:base':
  
      isFALSE
  
  > 
  > test_check("rngtools")
  ── 1. Failure: RNGtype (@test-format.R#100)  ───────────────────────────────────
  length(d) not identical to `expL`.
  1/1 mismatches
  [1] 3 - 2 == 1
  MISSING : result has correct length ( [ 2 ) ]
  
  ── 2. Failure: RNGtype (@test-format.R#101)  ───────────────────────────────────
  length(d) not identical to `expL`.
  1/1 mismatches
  [1] 3 - 2 == 1
  numeric(1) : result has correct length ( [ 2 ) Valid single numeric seed ]
  
  ── 3. Failure: RNGtype (@test-format.R#102)  ───────────────────────────────────
  length(d) not identical to `expL`.
  1/1 mismatches
  [1] 3 - 2 == 1
  integer(3) : result has correct length ( [ 2 ) Valid seed ]
  
  ── 4. Failure: RNGtype (@test-format.R#103)  ───────────────────────────────────
  length(d) not identical to `expL`.
  1/1 mismatches
  [1] 3 - 2 == 1
  integer(1) : result has correct length ( [ 2 ) Valid encoded kind ]
  
  ── 5. Failure: RNGtype (@test-format.R#106)  ───────────────────────────────────
  length(d) not identical to `expL`.
  1/1 mismatches
  [1] 3 - 2 == 1
  list(2) : result has correct length ( [ 2 ) list with rng slot ]
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 225 SKIPPED: 0 FAILED: 5
  1. Failure: RNGtype (@test-format.R#100) 
  2. Failure: RNGtype (@test-format.R#101) 
  3. Failure: RNGtype (@test-format.R#102) 
  4. Failure: RNGtype (@test-format.R#103) 
  5. Failure: RNGtype (@test-format.R#106) 
  
  Error: testthat unit tests failed
  Execution halted
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  5.1Mb
  sub-directories of 1Mb or more:
    doxygen   1.3Mb
    libs      3.1Mb
installed size is 100.6Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     98.4Mb
Namespace in Imports field not imported from: ‘impute’
  All declared Imports should be used.
Running ‘testthat.R’ [11s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rnn)
  > 
  > test_check("rnn")
  ── 1. Failure: (unknown) (@test_rnn.R#66)  ─────────────────────────────────────
  sum(bin2int(B)) not equal to 888626.
  1/1 mismatches
  [1] 374720 - 888626 == -513906
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test_rnn.R#66) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  18.5Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R  11.2Mb
Found the following significant warnings:
  ./hammock.h:369:15: warning: assigning field to itself [-Wself-assign-field]
See ‘/data/gannet/ripley/R/packages/tests-clang/robfilter.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'affydata', 'hgu95av2cdf', 'illuminaHumanv3.db'
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
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 21.4Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
File ‘robustHD/libs/robustHD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    libs  35.0Mb
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.
File ‘robustvarComp/libs/robustvarComp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
o.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
p.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
o.rocc: no visible global function definition for ‘prediction’
o.rocc: no visible global function definition for ‘performance’
o.rocc: no visible global function definition for ‘binom.test’
tr.rocc: no visible global function definition for ‘prediction’
tr.rocc: no visible global function definition for ‘performance’
Undefined global functions or variables:
  binom.test performance prediction
Consider adding
  importFrom("stats", "binom.test")
to your NAMESPACE file.
File ‘rollply/libs/rollply.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    libs  26.1Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘rstudioapi’ ‘tinytex’
  All declared Imports should be used.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.3Mb
    libs   5.7Mb
File ‘rotations/libs/rotations.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘utils’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rPackedBar)
  > 
  > test_check("rPackedBar")
  ── 1. Failure: object value (@test-gen_gray_bars.R#277)  ───────────────────────
  `test` not equivalent to `expected`.
  Component "bar_list": Component 1: Component 2: 1 string mismatch
  Component "bar_list": Component 1: Component 3: Component 1: 1 string mismatch
  Component "bar_list": Component 2: Component 2: 1 string mismatch
  Component "bar_list": Component 2: Component 3: Component 1: 1 string mismatch
  Component "bar_list": Component 3: Component 2: 1 string mismatch
  Component "bar_list": Component 3: Component 3: Component 1: 1 string mismatch
  Component "bar_list": Component 4: Component 2: 1 string mismatch
  Component "bar_list": Component 4: Component 3: Component 1: 1 string mismatch
  Component "bar_list": Component 5: Component 2: 1 string mismatch
  ...
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 43 SKIPPED: 0 FAILED: 1
  1. Failure: object value (@test-gen_gray_bars.R#277) 
  
  Error: testthat unit tests failed
  Execution halted
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  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      3.9Mb
File ‘Rphylopars/libs/Rphylopars.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   4.5Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   7.8Mb
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.
File ‘rrcovNA/libs/rrcovNA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.0Mb
  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:
  z.cpp:42:7: 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/rrpack.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘data.tree’ ‘penalized’
  All declared Imports should be used.
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.
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    dependencies  21.0Mb
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.
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘randomcoloR’
  All declared Imports should be used.
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.
Output from running autoconf:
  configure.ac:92: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
  ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
  ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from...
  ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from...
  ../../lib/autoconf/c.m4:1444: AC_C_BIGENDIAN is expanded from...
  configure.ac:92: the top level
  configure.ac:166: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
  ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
  ../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from...
  ../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from...
  configure.ac:166: the top level
Non-standard files/directories found at top level:
  ‘clients’ ‘clients.txt’ ‘version’
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.
File ‘rsgcc/libs/rsgcc.so’:
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’
File ‘rsgcc/libs/rsgcc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
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.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
installed size is 54.4Mb
  sub-directories of 1Mb or more:
    libs  53.8Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
Namespace in Imports field not imported from: ‘pkgconfig’
  All declared Imports should be used.
Running ‘testthat.R’ [57s/118s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("RSSL")
  Loading required package: RSSL
  ── 1. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#53)
  sum(predict(g_sup, problem$X_test) == problem$y_test) not equal to 61.
  1/1 mismatches
  [1] 55 - 61 == -6
  
  ── 2. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#54)
  sum(predict(g_semi, problem$X_test) == problem$y_test) not equal to 61.
  1/1 mismatches
  [1] 55 - 61 == -6
  
  ── 3. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#55)
  sum(predict(g_euc, problem$X_test) == problem$y_test) not equal to 57.
  1/1 mismatches
  [1] 55 - 57 == -2
  
  ── 4. Failure: Multiclass gives an output (@test-LeastSquaresClassifier.R#46)  ─
  sum(...) not equal to 61.
  1/1 mismatches
  [1] 60 - 61 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 466 SKIPPED: 0 FAILED: 4
  1. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#53) 
  2. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#54) 
  3. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#55) 
  4. Failure: Multiclass gives an output (@test-LeastSquaresClassifier.R#46) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 171.1Mb
  sub-directories of 1Mb or more:
    R       1.4Mb
    libs  168.1Mb
installed size is 286.5Mb
  sub-directories of 1Mb or more:
    libs  283.9Mb
installed size is 89.5Mb
  sub-directories of 1Mb or more:
    libs  88.2Mb
Namespace in Imports field not imported from: ‘loo’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
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
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  5.2Mb
  sub-directories of 1Mb or more:
    rmarkdown   5.0Mb
File ‘rtiff/libs/rtiff.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.8Mb
    projects   2.8Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
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.
Namespaces in Imports field not imported from:
  ‘DT’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   2.1Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   7.0Mb
File ‘runjags/libs/runjags.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RGtk2’
  All declared Imports should be used.
installed size is 44.0Mb
  sub-directories of 1Mb or more:
    libs  43.2Mb
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  5.4Mb
  sub-directories of 1Mb or more:
    include   5.4Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    include   2.6Mb
    libs      5.0Mb
installed size is 24.5Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
    test  19.6Mb
File ‘RWeightedKmeans/libs/RWeightedKmeans.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.8Mb
  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.
Found the following significant warnings:
  nchg.c:555:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/RxCEcolInf.Rcheck/00install.out’ for details.
File ‘RxCEcolInf/libs/RxCEcolInf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  11.2Mb
Namespace in Imports field not imported from: ‘n1qn1’
  All declared Imports should be used.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs    9.0Mb
    yacas   1.5Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    sample_data   3.1Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Namespace in Imports field not imported from: ‘spanel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘subplex’
  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.
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 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
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 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.6Mb
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.
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.
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘forecast’ ‘signal’
  All declared Imports should be used.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
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.
Namespace in Imports field not imported from: ‘pvclust’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
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.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/scio.Rcheck/00install.out’ for details.
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.
Namespace in Imports field not imported from: ‘shazam’
  All declared Imports should be used.
Running examples in ‘scorecardModelUtils-Ex.R’ failed
The error most likely occurred in:

> ### Name: scalling
> ### Title: Converting coefficients of logistic regression into scores for
> ###   scorecard building
> ### Aliases: scalling
> 
> ### ** Examples
> 
> data <- iris
> set.seed(11)
> data$Y <- sample(0:1,size=nrow(data),replace=TRUE)
> x <- c("Sepal.Length","Sepal.Width","Petal.Length","Petal.Width")
> iv_table_list <- iv_table(base = data,target = "Y",num_var_name = x,cat_var_name = "Species")
> num_cat <- num_to_cat(base = data,num_woe_table = iv_table_list$num_woe_table)
> log_model <- glm(Y ~ ., data = num_cat, family = "binomial")
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: glm ... model.matrix -> model.matrix.default -> contrasts<-
Execution halted
File ‘scorer/libs/scorer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Error(s) in re-building vignettes:
--- re-building ‘SDEFSRpackage.Rmd’ using rmarkdown
! Undefined control sequence.
l.1327 \textbackslash{}providecommand\{\doi
                                           \}\{doi: 
Here is how much of TeX's memory you used:
 13156 strings out of 493202
 192800 string characters out of 6146434
 302621 words of memory out of 5000000
 16577 multiletter control sequences out of 15000+600000
 64247 words of font info for 121 fonts, out of 8000000 for 9000
 805 hyphenation exceptions out of 8191
 32i,7n,38p,976b,470s stack positions out of 5000i,500n,10000p,200000b,80000s

Error: processing vignette 'SDEFSRpackage.Rmd' failed with diagnostics:
Failed to compile SDEFSRpackage.tex. See SDEFSRpackage.log for more info.
--- failed re-building ‘SDEFSRpackage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
Found the following significant warnings:
  pointinpolygon.c:60:7: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:33: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:50:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:126:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/SDMTools.Rcheck/00install.out’ for details.
File ‘SDMTools/libs/SDMTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’ ‘tidyr’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: ‘__var_1_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/sdwd.Rcheck/00install.out’ for details.
File ‘sdwd/libs/sdwd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R   7.2Mb
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 ‘seedy-Ex.R’ failed
The error most likely occurred in:

> ### Name: simulateoutbreak
> ### Title: Simulate transmission and evolutionary dynamics
> ### Aliases: simulateoutbreak
> 
> ### ** Examples
> 
> 
> W <- simulateoutbreak(init.sus=10, inf.rate=0.002, rem.rate=0.001, mut.rate=0.0001, 
+                       equi.pop=2000, inoc.size=1, samples.per.time=10, 
+                       samp.schedule="calendar", samp.freq=500, mincases=3) 

Simulating outbreak:
N=2000, b=1, beta=0.002, gamma=0.001, mu=1e-04

Attempt 1
t=500, S=10, I=1, total genotypes=3, next rec time=747
t=1000, S=8, I=1, total genotypes=6, next rec time=1035
t=1035, S=8, I=0, total genotypes=0
Insufficient number of infections! (mincases=3)
Attempt 2
t=500, S=10, I=1, total genotypes=3, next rec time=833
t=1000, S=9, I=1, total genotypes=2, next rec time=5629
Error in strain.log[[newinfect]] <- unique(inoc.samp) : 
  attempt to select more than one element in integerOneIndex
Calls: simulateoutbreak
Execution halted
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: ‘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’
plot.SEL: no visible global function definition for ‘plot’
print.SEL: no visible global function definition for ‘integrate’
print.summary.SEL : foo1: no visible global function definition for
  ‘predict’
print.summary.SEL : foo2: no visible global function definition for
  ‘predict’
print.summary.SEL: no visible global function definition for
  ‘integrate’
quantSEL: no visible global function definition for ‘predict’
quantSEL: no visible global function definition for ‘splinefun’
rvSEL: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbeta dbinom integrate pbeta plot predict runif splinefun uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dbeta", "dbinom", "integrate", "pbeta", "predict",
             "runif", "splinefun", "uniroot")
to your NAMESPACE file.
File ‘SEL/libs/SEL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lavaan’ ‘psych’ ‘semPlot’ ‘semTools’ ‘shinyAce’
  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.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘XML’ ‘mgcv’
  All declared Imports should be used.
Running ‘testthat.R’ [15s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("sentimentr")
  > 
  > test_check("sentimentr")
  OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
  OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  ── 1. Failure: extract_sentiment_terms extracts the terms (@test-extract_sentime
  pol_words$negative[1:3] not equal to list(character(0), c("wait", "restless", "fire"), character(0)).
  Component 2: Lengths (0, 3) differ (string compare on first 0)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 32 SKIPPED: 0 FAILED: 1
  1. Failure: extract_sentiment_terms extracts the terms (@test-extract_sentiment_terms.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.8Mb
File ‘seqCBS/libs/seqCBS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs  13.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
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 25.7Mb
  sub-directories of 1Mb or more:
    libs  24.3Mb
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 18.4Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
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', 'MAST'
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    doc     11.2Mb
    libs     7.1Mb
    sqlite   1.5Mb
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  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.0Mb
Namespaces in Imports field not imported from:
  ‘parallel’ ‘plyr’
  All declared Imports should be used.
File ‘sharpeRratio/libs/sharpeRratio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
Namespace in Imports field not imported from: ‘shinydashboard’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘htmlwidgets’ ‘jsonlite’ ‘viridis’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘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.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    www   8.0Mb
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.
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.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sigmajs)
  Welcome to sigmajs
  
  Docs: sigmajs.john-coene.com
  > 
  > test_check("sigmajs")
  Found # 4 clusters
  ── 1. Failure: delay (@test-graph.R#50)  ───────────────────────────────────────
  unlist(unname(sg$x$addNodesDelay[[1]][5])) not equal to " 566.004".
  1/1 mismatches
  x[1]: " 548.9736"
  y[1]: " 566.004"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 65 SKIPPED: 0 FAILED: 1
  1. Failure: delay (@test-graph.R#50) 
  
  Error: testthat unit tests failed
  Execution halted
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  7.7Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘MASS’ ‘class’ ‘cluster’ ‘lattice’ ‘nnet’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(simcdm)
  > 
  > test_check("simcdm")
  ── 1. Failure: Simulation of attributes matches (@test-attributes.R#71)  ───────
  `subject_alphas_func` not equal to `subject_alphas_base`.
  34/60 mismatches (average diff: 1)
  [1]  0 - 1 == -1
  [3]  0 - 1 == -1
  [4]  1 - 0 ==  1
  [5]  1 - 0 ==  1
  [6]  0 - 1 == -1
  [10] 1 - 0 ==  1
  [12] 0 - 1 == -1
  [14] 0 - 1 == -1
  [15] 1 - 0 ==  1
  ...
  Equivalent subject alpha Generation
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 14 SKIPPED: 0 FAILED: 1
  1. Failure: Simulation of attributes matches (@test-attributes.R#71) 
  
  Error: testthat unit tests failed
  Execution halted
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.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  13.2Mb
Namespace in Imports field not imported from: ‘quadprog’
  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.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(SimplifyStats)
  > 
  > test_check("SimplifyStats")
  
  The Shapiro-Wilk test requires 3 < N < 5000.
  
  ── 1. Failure: valid input produce valid output (@test.group_summarize.R#34)  ──
  {
      ...
  } isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 8 SKIPPED: 0 FAILED: 1
  1. Failure: valid input produce valid output (@test.group_summarize.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.0Mb
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.
Namespaces in Imports field not imported from:
  ‘BB’ ‘MASS’ ‘ggplot2’ ‘grid’ ‘triangle’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pracma’
  All declared Imports should be used.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   6.3Mb
Namespace in Imports field not imported from: ‘mcmc’
  All declared Imports should be used.
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.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.2Mb
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 49.5Mb
  sub-directories of 1Mb or more:
    libs  48.0Mb
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 ‘slfm/libs/slfm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Running ‘testthat.R’ [13s/38s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(slouch)
  > 
  > # testsetup <- function(){
  > #   pars <- list(myfunc = myfunc, dummydata = dummydata, model.id.btk = model.id.btk)
  > #   return(pars)
  > # }
  > 
  > test_check("slouch")
  ── 1. Failure: No errors ANOVA (@test_anova.R#37)  ─────────────────────────────
  structure(...) not equal to m1$beta_primary$coefficients.
  3/4 mismatches (average diff: 0.0444)
  [1] 0.4216 - 0.4893 == -0.06774
  [2] 0.4815 - 0.4220 ==  0.05951
  [4] 0.0504 - 0.0445 ==  0.00591
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 9 SKIPPED: 0 FAILED: 1
  1. Failure: No errors ANOVA (@test_anova.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
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
File ‘smac/libs/smac.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(SmartEDA)
  > 
  > 
  > context("Summary statistics")
  > 
  > test_that("ExpKurtosis and ExpSkew are measures of shapes value", {
  +   expect_equal(ExpKurtosis(c(1:4),type="moment"), 1.64)
  +   set.seed(1234)
  +   expect_equal(ExpSkew(sample(1:100,10),type="moment"),-0.2131082)
  + })
  Error: Test failed: 'ExpKurtosis and ExpSkew are measures of shapes value'
  * ExpSkew(sample(1:100, 10), type = "moment") not equal to -0.2131082.
  1/1 mismatches
  [1] 0.618 - -0.213 == 0.831
  Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
Found the following significant warnings:
  MCP_efficient.c:114:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:134:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:154:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/SMCP.Rcheck/00install.out’ for details.
File ‘SMCP/libs/SMCP.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SMC/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.
Running ‘testthat.R’ [4s/50s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # setting R_TESTS to empty string because of
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # revert this when that issue in R is fixed.
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(Smisc)
  > 
  > # There shouldn't be any files in the tmp folder
  > unlink("testthat/tmp", recursive = TRUE, force = TRUE)
  > dir.create("testthat/tmp")
  > 
  > test_check("Smisc")
  ── 1. Failure: parseJob() doesn't deviate from historical behavior (@test_parseJ
  `xout` not equal to `xin`.
  Component "x2": Component 1: Mean relative difference: 0.8461538
  Component "x2": Component 2: Mean relative difference: 0.7532468
  Component "x2": Component 3: Mean relative difference: 0.5416667
  Component "x2": Component 4: Mean relative difference: 0.34375
  Component "x2": Component 5: Mean relative difference: 0.5441176
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 275 SKIPPED: 0 FAILED: 1
  1. Failure: parseJob() doesn't deviate from historical behavior (@test_parseJob.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   7.9Mb
File ‘sna/libs/sna.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
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.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("SOMbrero")
  Loading required package: igraph
  
  Attaching package: 'igraph'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  The following objects are masked from 'package:stats':
  
      decompose, spectrum
  
  The following object is masked from 'package:base':
  
      union
  
  
  ***********************************************************
  
        This is 'SOMbrero' package, v 1.2
  
  Citation details with citation('SOMbrero')
  
  Further information with help(SOMbrero)...
  
  Use sombreroGUI() to start the Graphical Interface.
  
  ***********************************************************
  > 
  > test_check("SOMbrero")
  ── 1. Failure: case relational - radius 'letremy' and affectation 'heskes' (@tes
  predict(rsom, dissim.lesmis) not equal to rsom$clustering.
  2/77 mismatches (average diff: 6)
  [44] 22 - 16 == 6
  [56] 22 - 16 == 6
  
  ── 2. Failure: case relational - radius 'letremy' and affectation 'heskes' (@tes
  predict(rsom) not equal to rsom$clustering.
  2/77 mismatches (average diff: 6)
  [44] 22 - 16 == 6
  [56] 22 - 16 == 6
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 26 SKIPPED: 0 FAILED: 2
  1. Failure: case relational - radius 'letremy' and affectation 'heskes' (@test-prediction.R#61) 
  2. Failure: case relational - radius 'letremy' and affectation 'heskes' (@test-prediction.R#63) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   5.4Mb
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 ‘soobench/libs/soobench.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Namespaces in Imports field not imported from:
  ‘gtools’ ‘hashmap’ ‘reshape2’
  All declared Imports should be used.
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 ‘spacejam/libs/spacejam.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘rstudioapi’
  All declared Imports should be used.
Running ‘test-all.R’ [93s/121s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.tools")
  Loading required package: SpaDES.tools
  OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
  OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  ── 1. Failure: spread produces legal RasterLayer (@test-spread.R#60)  ──────────
  all(...) isn't true.
  
  ── 2. Failure: spreadProb with relative values does not work correctly (@test-sp
  sum(hab3[events1[] > 0]) > sum(hab3[events2[] > 0]) isn't true.
  
  ── 3. Failure: spread2 tests (@test-spread2.R#220)  ────────────────────────────
  cht$p.value > 0.05 isn't true.
  
  [1] "Scales with number of starts, not maxSize of raster"
  ── 4. Failure: spread2 tests -- asymmetry (@test-spread2.R#710)  ───────────────
  circs[sams] == circs[ciCentre[] == 1] isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1048 SKIPPED: 11 FAILED: 4
  1. Failure: spread produces legal RasterLayer (@test-spread.R#60) 
  2. Failure: spreadProb with relative values does not work correctly (@test-spread.R#1259) 
  3. Failure: spread2 tests (@test-spread2.R#220) 
  4. Failure: spread2 tests -- asymmetry (@test-spread2.R#710) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 35.8Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs  33.6Mb
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
Running examples in ‘spa-Ex.R’ failed
The error most likely occurred in:

> ### Name: predict.spa
> ### Title: Inductive Predict Procedure For SPA
> ### Aliases: predict.spa
> ### Keywords: classes models methods
> 
> ### ** Examples
> 
> ## Use simulated example (two moon) and generate a contour plot of the border
> set.seed(100)
> dat=spa.sim(type="moon") 
> 
> L=which(!is.na(dat$y))
> U=which(is.na(dat$y))
> Dij=as.matrix(daisy(dat[,-1]))
> 
> ##Use spa to train with a supervised/transductive kernel smoother
> gsup<-spa(dat$y[L],graph=Dij[L,L],control=spa.control(gcv="lGCV"))
Error in if (g1 < g2) { : missing value where TRUE/FALSE needed
Calls: spa -> spa.gcv
Execution halted
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 ‘sparc/libs/sparc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
File ‘sparseLTSEigen/libs/sparseLTSEigen.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  15.8Mb
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.
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    R      5.1Mb
    doc    4.8Mb
    help   5.0Mb
    libs   2.0Mb
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    libs  27.9Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
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  6.5Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
File ‘SpeciesMix/libs/SpeciesMix.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘usethis’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘Spectrum_vignette.Rmd’ using rmarkdown
tlmgr search --file --global '/framed.sty'
TeX Live 2018 is frozen forever and will no
longer be updated.  This happens in preparation for a new release.

If you're interested in helping to pretest the new release (when
pretests are available), please read https://tug.org/texlive/pretest.html.
Otherwise, just wait, and the new release will be ready in due time.
Trying to automatically install missing LaTeX packages...
tlmgr install framed
TeX Live 2018 is frozen forever and will no
longer be updated.  This happens in preparation for a new release.

If you're interested in helping to pretest the new release (when
pretests are available), please read https://tug.org/texlive/pretest.html.
Otherwise, just wait, and the new release will be ready in due time.
tlmgr: package repository http://mirror.ox.ac.uk/sites/ctan.org/systems/texlive/tlnet (verified)
tlmgr install: package already present: framed
tlmgr path add
add_link_dir_dir: /usr/local/share/info/dir exists; not making symlink.
tlmgr search --file --global '/framed.sty'
TeX Live 2018 is frozen forever and will no
longer be updated.  This happens in preparation for a new release.

If you're interested in helping to pretest the new release (when
pretests are available), please read https://tug.org/texlive/pretest.html.
Otherwise, just wait, and the new release will be ready in due time.
! LaTeX Error: File `framed.sty' not found.

! Emergency stop.
<read *> 

Error: processing vignette 'Spectrum_vignette.Rmd' failed with diagnostics:
Failed to compile Spectrum_vignette.tex. See Spectrum_vignette.log for more info.
--- failed re-building ‘Spectrum_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
Namespace in Imports field not imported from: ‘maptools’
  All declared Imports should be used.
Running ‘testthat.R’ [32s/41s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(spew)
  > 
  > test_check("spew")
  OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
  OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  ── 1. Error: Moment Matching (@test-sampling.R#32)  ────────────────────────────
  abs(2.8 - mean(pums[inds, ]$NP)) < 0.05 is not TRUE
  1: stopifnot(abs(2.8 - mean(pums[inds, ]$NP)) < 0.05) at testthat/test-sampling.R:32
  
  [1] "Place has 0 Households!"
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 101 SKIPPED: 7 FAILED: 1
  1. Error: Moment Matching (@test-sampling.R#32) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’
  All declared Imports should be used.
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    libs  25.0Mb
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.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(splitstackshape)
  > 
  > test_check("splitstackshape")
  OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
  OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  ── 1. Failure: stratified returns the expected number of rows (@test_stratified.
  nrow(stratified(DF, "A", 0.1, select = list(A = c("AA", "BB")))) not equal to 3.
  1/1 mismatches
  [1] 4 - 3 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 51 SKIPPED: 0 FAILED: 1
  1. Failure: stratified returns the expected number of rows (@test_stratified.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
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.
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 14.4Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   8.2Mb
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘ggplot2’
  All declared Imports should be used.
File ‘SPSL/libs/SPSL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  14.3Mb
Namespaces in Imports field not imported from:
  ‘BayesX’ ‘BayesXsrc’ ‘automap’ ‘plyr’ ‘rgdal’ ‘splines’
  All declared Imports should be used.
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.
File ‘SSL/libs/SSL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 78.0Mb
  sub-directories of 1Mb or more:
    libs  77.7Mb
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:
round(sum(datasub$value, na.rm = TRUE), 2) and round(sum(datasub2$value, na.rm = TRUE), 2) are not equal:
  Mean relative difference: 0.000996741
--- 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 12.3Mb
  sub-directories of 1Mb or more:
    include   9.9Mb
    lib       2.4Mb
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.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   4.9Mb
Namespace in Imports field not imported from: ‘MCMCpack’
  All declared Imports should be used.
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 15.0Mb
  sub-directories of 1Mb or more:
    doc  10.3Mb
    nc    3.5Mb
Error(s) in re-building vignettes:
--- re-building ‘HTML_special_features.Rmd’ using rmarkdown
--- finished re-building ‘HTML_special_features.Rmd’

--- re-building ‘Rmarkdown.Rmd’ using rmarkdown
pandoc: Cannot decode byte '\xa9': Data.Text.Internal.Encoding.streamDecodeUtf8With: Invalid UTF-8 stream
Error: processing vignette 'Rmarkdown.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
--- failed re-building ‘Rmarkdown.Rmd’

--- re-building ‘code_chunks.Rmd’ using rmarkdown
OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
pandoc: Cannot decode byte '\xa9': Data.Text.Internal.Encoding.streamDecodeUtf8With: Invalid UTF-8 stream
Error: processing vignette 'code_chunks.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
--- failed re-building ‘code_chunks.Rmd’

--- re-building ‘stationery.Rnw’ using Sweave
--- finished re-building ‘stationery.Rnw’

SUMMARY: processing the following files failed:
  ‘Rmarkdown.Rmd’ ‘code_chunks.Rmd’

Error: Vignette re-building failed.
Execution halted
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:
  ‘dplyr’ ‘ggplot2’ ‘stringr’
  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.
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 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
File ‘stepwise/libs/stepwise.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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  7.6Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   4.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R          2.1Mb
    datasets   2.6Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespace in Imports field not imported from: ‘knitcitations’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘boot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Namespace in Imports field not imported from: ‘hexbin’
  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.
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 11.6Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   9.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Namespaces in Imports field not imported from:
  ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   2.9Mb
File ‘strum/libs/strum.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Running ‘test-all.R’ [23s/55s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("STV")
  Loading required package: STV
  ── 1. Failure: Toy example (@testExt.R#36)  ────────────────────────────────────
  `x` not equal to `expected`.
  1/4 mismatches
  x[2]: "ATL_54"
  y[2]: "ATL_27"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 4 SKIPPED: 0 FAILED: 1
  1. Failure: Toy example (@testExt.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘UpSetR’ ‘alluvial’ ‘geoR’ ‘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.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    2.5Mb
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.
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.
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/SuppDists.Rcheck/00install.out’ for details.
File ‘SuppDists/libs/SuppDists.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘matrixStats’ ‘nloptr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DiceOptim’ ‘GPareto’ ‘rgenoud’
  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  8.2Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   1.6Mb
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 160.5Mb
  sub-directories of 1Mb or more:
    libs  159.1Mb
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.
Namespace in Imports field not imported from: ‘cowplot’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
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.
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.
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.
Found the following significant warnings:
  trlan/trlcore.c:983:15: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlcore.c:1642:9: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlcore.c:1642:20: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlaux.c:28:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:41:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:62:13: warning: comparison of array 'info->cpfile' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlan.c:171:20: warning: comparison of array 'info->oldcpf' equal to a null pointer is always false [-Wtautological-pointer-compare]
  trlan/ztrlcore.c:1418:12: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/svd.Rcheck/00install.out’ for details.
File ‘svmadmm/libs/svmadmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘svmpath/libs/svmpath.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi30spec.o’, ‘mi35mps.o’,
      ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘_gfortran_st_rewind’, possibly from ‘rewind’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi10unix.o’, ‘mi35mps.o’, ‘mi40bfil.o’
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’
File ‘svmpath/libs/svmpath.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Different type kinds at (1)
  Warning: GNU Extension: initialization of common block variable ‘iset’ in DATA statement at (1)
  Warning: GNU Extension: Variable ‘iset’ at (1) is in COMMON but only in BLOCK DATA initialization is allowed
  Warning: GNU Extension: Missing comma at (1)
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1) [-Wcharacter-truncation]
  Warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘cnop’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1) [-Wcharacter-truncation]
  Warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/SWATmodel.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘lazyeval’ ‘lubridate’ ‘tidyr’
  All declared Imports should be used.
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.
Running examples in ‘synthpop-Ex.R’ failed
The error most likely occurred in:

> ### Name: syn.satcat
> ### Title: Synthesis from a saturated model based on all combinations of
> ###   the predictor variables.
> ### Aliases: syn.satcat
> ### Keywords: datagen
> 
> ### ** Examples
> 
> ods <- SD2011[, c("region", "sex", "agegr", "placesize")]
> 
> s1 <- syn(ods, method = c("sample", "cart", "satcat", "cart"))
Synthesis
-----------
 region sex agegr placesize
> 
> ### mostly fails because too many small categories
> s2 <- syn(ods, method = c("sample", "cart", "cart", "satcat"))  
Synthesis
-----------
 region sex agegr placesize

syn.categories
   Malopolskie-FEMALE-NAtemp   Podkarpackie-FEMALE-NAtemp 
                           1                            1 
Swietokrzyskie-FEMALE-NAtemp 
                           1 
Error: The combined groups above for "satcat" have no records in original data.

         Consider using grouped synthesis with "syn.catall" to overcome this
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
Namespace in Imports field not imported from: ‘iterators’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tidyr’
  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.
File ‘tailDepFun/libs/tailDepFun.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘devEMF’ ‘segmented’ ‘smoother’ ‘tools’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   4.6Mb
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.
Running ‘testthat.R’ [180s/504s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(TauStar)
  > 
  > test_check("TauStar")
  ── 1. Failure: tauStarTest with mixed data. (@test_tauStarTest.R#89)  ──────────
  abs(a$pVal - (1 - pMixHoeffInd(n * tval, p))) <= 10^-2 isn't true.
  
  ── 2. Failure: tauStarTest with mixed data. (@test_tauStarTest.R#89)  ──────────
  abs(a$pVal - (1 - pMixHoeffInd(n * tval, p))) <= 10^-2 isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 529 SKIPPED: 0 FAILED: 2
  1. Failure: tauStarTest with mixed data. (@test_tauStarTest.R#89) 
  2. Failure: tauStarTest with mixed data. (@test_tauStarTest.R#89) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘knitr’ ‘lazyeval’ ‘rlang’ ‘tidyr’
  All declared Imports should be used.
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.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tbltools)
  > 
  > test_check("tbltools")
  ── 1. Failure: filter_data, arrange_data (@test-tbl.R#60)  ─────────────────────
  nrow(filter_data(d, d$abc == "a")) not equal to 34.
  1/1 mismatches
  [1] 30 - 34 == -4
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 99 SKIPPED: 0 FAILED: 1
  1. Failure: filter_data, arrange_data (@test-tbl.R#60) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    tklibs   4.9Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.9Mb
installed size is 37.2Mb
  sub-directories of 1Mb or more:
    libs  35.9Mb
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
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.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    apps   2.8Mb
    libs   8.6Mb
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  16.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
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.
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.
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  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Found the following significant warnings:
  GloveFitter.cpp:80:7: warning: explicitly assigning value of variable of type 'GloveFit' to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/text2vec.Rcheck/00install.out’ for details.
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.6Mb
    libs   5.5Mb
Namespace in Imports field not imported from: ‘irlba’
  All declared Imports should be used.
Note: found 10051 marked UTF-8 strings
  Note: found 10523 strings marked as "bytes"
Namespace in Imports field not imported from: ‘lexicon’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘forecast’ ‘lars’ ‘parallel’ ‘tau’ ‘tsDyn’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
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 16.2Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
File ‘tgcd/libs/tgcd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    rda    7.1Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘splancs’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘broom’ ‘dials’ ‘parsnip’
  All declared Imports should be used.
installed size is  5.2Mb
  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.
Namespaces in Imports field not imported from:
  ‘dbplyr’ ‘reprex’ ‘rlang’
  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 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
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.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘forecast’
  All declared Imports should be used.
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.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc         3.7Mb
    rmarkdown   1.3Mb
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 18.4Mb
  sub-directories of 1Mb or more:
    examples  15.0Mb
    include    3.0Mb
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    libs  26.5Mb
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.
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.
Note: found 64 marked Latin-1 strings
  Note: found 548 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘shinyAce’ ‘shinycssloaders’ ‘shinydashboard’
  All declared Imports should be used.
Running examples in ‘TPmsm-Ex.R’ failed
The error most likely occurred in:

> ### Name: transLS
> ### Title: Location-Scale transition probabilities
> ### Aliases: transLS
> ### Keywords: dplot nonparametric smooth survival
> 
> ### ** Examples
> 
> # Set the number of threads
> nth <- setThreadsTP(2)
> 
> # Create survTP object
> data(bladderTP)
> bladderTP_obj <- with(bladderTP, survTP(time1, event1, Stime, event))
> 
> # Compute transition probabilities
> LS0 <- transLS(object=bladderTP_obj, s=5, t=59, h=c(0.25, 2.5), nh=25, ncv=50, conf=FALSE)
> print(LS0)
Location-Scale transition probabilities

Estimates of P(5, 59)
          1         2         3
1 0.5036414 0.1602728 0.3360858
2 0.0000000 0.3617209 0.6382791
3 0.0000000 0.0000000 1.0000000
> 
> # Compute transition probabilities with confidence band
> h <- with( LS0, c( rep(h[1], 2), rep(h[2], 2) ) )
> transLS(object=bladderTP_obj, s=5, t=59, h=h, conf=TRUE,
+ conf.level=0.95, method.boot="percentile", boot.cv=FALSE)

 *** caught segfault ***
address 0x88, cause 'memory not mapped'

Traceback:
 1: TransPROB.LS(object, UT, nboot = nboot, ...)
 2: TransPROB(object, UT, nboot = nboot, ...)
 3: TPBoot.cboot(object, UT, n.boot, ...)
 4: TPBoot(object, UT, n.boot, ...)
 5: TransBoot.TP(object, s, t, state.names, n.boot, conf.level, method.boot,     ...)
 6: TransBoot(object, s, t, state.names, n.boot, conf.level, method.boot,     ...)
 7: TransMethod.TP(object, s, t, state.names, conf, n.boot, conf.level,     method.boot, h = h, nh = nh, ncv = ncv, window = window,     bootcv = boot.cv, cvfull = cv.full)
 8: TransMethod(object, s, t, state.names, conf, n.boot, conf.level,     method.boot, h = h, nh = nh, ncv = ncv, window = window,     bootcv = boot.cv, cvfull = cv.full)
 9: transLS(object = bladderTP_obj, s = 5, t = 59, h = h, conf = TRUE,     conf.level = 0.95, method.boot = "percentile", boot.cv = FALSE)
An irrecoverable exception occurred. R is aborting now ...
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.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    data      2.1Mb
    doc       2.7Mb
    extdata   8.4Mb
Namespace in Imports field not imported from: ‘neuralnet’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘lme4’ ‘nlme’
  All declared Imports should be used.
File ‘treeclim/libs/treeclim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

> ### Name: sim.bd.age
> ### Title: sim.bd.age: Simulating birth-death trees of a fixed age.
> ### Aliases: sim.bd.age
> 
> ### ** Examples
> 
> age<-2
> lambda <- 2.0
> mu <- 0.5
> frac <-0.6
> numbsim<-3
> 
> ##
> # Simulating trees with time age since the origin:
> 
> sim.bd.age(age,numbsim,lambda,mu,mrca=FALSE,complete=TRUE)
[[1]]

Phylogenetic tree with 117 tips and 116 internal nodes.

Tip labels:
	t51, t46, t102, t11, t8, t87, ...

Rooted; includes branch lengths.

[[2]]
[1] 0

[[3]]
[1] 0

> sim.bd.age(age,numbsim,lambda,mu,frac,mrca=FALSE,complete=FALSE)
Warning in max(oldnodes) :
  no non-missing arguments to max; returning -Inf
Error in integer(max(oldnodes)) : vector size cannot be infinite
Calls: sim.bd.age ... drop.extinct -> .drop.tip -> collapse.singles -> integer
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
installed size is 55.9Mb
  sub-directories of 1Mb or more:
    libs  54.3Mb
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.
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.
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.
File ‘tripack/libs/tripack.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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
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  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
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.
Namespace in Imports field not imported from: ‘gsDesign’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘forecast’
  All declared Imports should be used.
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.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
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: ‘colormap’
  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.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/uavRst.Rcheck/00install.out’ for details.
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.
installed size is 31.4Mb
  sub-directories of 1Mb or more:
    doc         5.3Mb
    dummydata   1.4Mb
    libs       23.5Mb
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.
Namespace in Imports field not imported from: ‘viridis’
  All declared Imports should be used.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    8.3Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
Running ‘test_unifDAG.R’ [6s/15s]
Running the tests in ‘tests/test_unifDAG.R’ failed.
Complete output:
  > library(unifDAG)
  > 
  > my.wgtMatrix <- function(g, transpose = TRUE) {
  +   res <- as(g, "matrix") # from 'graph' package, now reliable (we hope)
  +   if (transpose) ## default!
  +     t(res) else res
  + }
  > 
  > ## exact
  > set.seed(123)
  > n <- 2
  > reps <- 100
  > res <- matrix(0, reps, 3)
  > for (i in 1:reps) {
  +     gAM <- unifDAG(n)
  +     wm <- my.wgtMatrix(gAM)
  +     if (wm[1,2] != 0) {
  +         res[i,1] <- 1
  +     } else {
  +           if (wm[2,1] != 0) {
  +               res[i,2] <- 1
  +           } else {
  +                 res[i,3] <- 1
  +             }
  +       }
  + }
  > if (!all(round(colMeans(res), 2) == c(0.41, 0.31, 0.28))) {
  +     stop("test_unifDAG: Saved result could not be reproduced (unifDAG).")
  + }
  Error: test_unifDAG: Saved result could not be reproduced (unifDAG).
  Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    1.6Mb
    libs   4.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Namespace in Imports field not imported from: ‘mcmcplots’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
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.
Running examples in ‘urltools-Ex.R’ failed
The error most likely occurred in:

> ### Name: tld_extract
> ### Title: Extract TLDs
> ### Aliases: tld_extract
> 
> ### ** Examples
> 
> # Using the inbuilt dataset
> domains <- domain("https://en.wikipedia.org/wiki/Main_Page")
> tld_extract(domains)
            domain tld
1 en.wikipedia.org org
> 
> # Using a refreshed one
> tld_extract(domains, tld_refresh())
Warning in file(con, "r") :
  cannot open URL 'http://data.iana.org/TLD/tlds-alpha-by-domain.txt': HTTP status was '403 Forbidden'
Error in file(con, "r") : 
  cannot open the connection to 'http://data.iana.org/TLD/tlds-alpha-by-domain.txt'
Calls: tld_extract -> tld_refresh -> readLines -> file
Execution halted
File ‘uroot/libs/uroot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    data  26.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   6.2Mb
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘stringdist’ ‘utils’
  All declared Imports should be used.
Running ‘testthat.R’ [27s/50s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(utiml)
  Loading required package: mldr
  Loading required package: parallel
  > 
  > test_check("utiml")
  ── 1. Failure: Bipartition measures (@test_evaluation.R#153)  ──────────────────
  mean(utiml_measure_macro_f1(mlconfmat)) not equal to measures$MacroFMeasure.
  1/1 mismatches
  [1] 0.275 - NaN == NaN
  
  ── 2. Failure: iterative kfold (@test_sampling.R#238)  ─────────────────────────
  length(f1$fold[[2]]) not equal to 25.
  1/1 mismatches
  [1] 24 - 25 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1155 SKIPPED: 21 FAILED: 2
  1. Failure: Bipartition measures (@test_evaluation.R#153) 
  2. Failure: iterative kfold (@test_sampling.R#238) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘uuid/libs/uuid.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘gen_uuid.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘gen_uuid.o’
File ‘uuid/libs/uuid.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("vanddraabe")
  Loading required package: vanddraabe
  ── 1. Failure: the correct mobility values are returned (@test-BoundWaterEnviron
  Mobility(Bvalues, occupancy) not equal to `mobility.answer`.
  14/14 mismatches (average diff: 0.0382)
  [1] 0.224 - 0.225 == -0.00168
  [2] 0.373 - 0.375 == -0.00280
  [3] 0.471 - 0.474 == -0.00354
  [4] 0.621 - 0.626 == -0.00467
  [5] 0.706 - 0.676 ==  0.03025
  [6] 0.824 - 0.876 == -0.05229
  [7] 0.993 - 0.948 ==  0.04521
  [8] 1.006 - 1.013 == -0.00756
  [9] 1.242 - 1.126 ==  0.11578
  ...
  
  ── 2. Failure: counting AtomTypes works (@test-utilities.R#102)  ───────────────
  getAtomTypeCounts(atom.types) not equal to `ATCounts.answer`.
  56/167 mismatches (average diff: 5.09)
  [4]  0 - 1 == -1
  [9]  0 - 8 == -8
  [11] 0 - 7 == -7
  [14] 7 - 1 ==  6
  [15] 1 - 0 ==  1
  [18] 0 - 1 == -1
  [21] 0 - 1 == -1
  [23] 0 - 4 == -4
  [31] 1 - 0 ==  1
  ...
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 63 SKIPPED: 0 FAILED: 2
  1. Failure: the correct mobility values are returned (@test-BoundWaterEnvironments.R#71) 
  2. Failure: counting AtomTypes works (@test-utilities.R#102) 
  
  Error: testthat unit tests failed
  Execution halted
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 10.7Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
File ‘vbdm/libs/vbdm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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  7.5Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
File ‘VDA/libs/VDA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘maptools’ ‘rgeos’
  All declared Imports should be used.
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  26.9Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    doc    1.2Mb
    help   2.8Mb
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.
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.
Running examples in ‘virtualspecies-Ex.R’ failed
The error most likely occurred in:

> ### Name: generateRandomSp
> ### Title: Generate a random virtual species distribution from
> ###   environmental variables
> ### Aliases: generateRandomSp
> 
> ### ** Examples
> 
> # Create an example stack with six environmental variables
> a <- matrix(rep(dnorm(1:100, 50, sd = 25)), 
+             nrow = 100, ncol = 100, byrow = TRUE)
> env <- stack(raster(a * dnorm(1:100, 50, sd = 25)),
+              raster(a * 1:100),
+              raster(a * logisticFun(1:100, alpha = 10, beta = 70)),
+              raster(t(a)),
+              raster(exp(a)),
+              raster(log(a)))
> names(env) <- paste("Var", 1:6, sep = "")   
> 
> # More than 6 variables: by default a PCA approach will be used
> generateRandomSp(env)
 - Perfoming the pca

 - Defining the response of the species along PCA axes

 - Calculating suitability values

 - Converting into Presence - Absence

   --- Determing species.prevalence automatically according to alpha and beta


Virtual species generated from 6 variables:
 Var1, Var2, Var3, Var4, Var5, Var6

- Approach used: Response to axes of a PCA
- Axes:  1, 2 ;  81.71 % explained by these axes
- Responses to axes:
   .Axis 1  [min=-3.52; max=3.55] : dnorm (mean=1.399218; sd=2.969177)
   .Axis 2  [min=-1.74; max=3.75] : dnorm (mean=0.2190712; sd=1.881691)
- Environmental suitability was rescaled between 0 and 1

- Converted into presence-absence:
   .Method = probability
   .alpha (slope)           = -0.1
   .beta  (inflexion point) = 0.128128128128128
   .species prevalence      = 0.914> 
> # Manually choosing a response approach
> generateRandomSp(env, approach = "response")
 - Determining species' response to predictor variables

Error in seq.default(cur.rast@data@min, cur.rast@data@max, length = 1000) : 
  'from' must be a finite number
Calls: generateRandomSp -> sample -> seq -> seq.default
Execution halted
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc           5.6Mb
    htmlwidgets   4.0Mb
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘iterators’ ‘knitr’ ‘purrr’ ‘testthat’
  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:
  ‘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 56.6Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  54.5Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ENMeval’ ‘RColorBrewer’ ‘XML’ ‘dismo’ ‘dplyr’ ‘leaflet.extras’
  ‘maptools’ ‘raster’ ‘rgdal’ ‘rgeos’ ‘rmarkdown’ ‘shinyjs’
  ‘shinythemes’ ‘spThin’ ‘spocc’ ‘zip’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
File ‘wand/libs/wand.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   4.0Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc  12.1Mb
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.
File ‘waveslim/libs/waveslim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Namespace in Imports field not imported from: ‘moonBook’
  All declared Imports should be used.
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    doc   11.9Mb
    libs   1.2Mb
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.
Found the following significant warnings:
  t_region.cpp:78:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:115:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:120:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/WhopGenome.Rcheck/00install.out’ for details.
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  17.0Mb
File ‘widals/libs/widals.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘wikisourcer.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

Quitting from lines 78-81 (wikisourcer.Rmd) 
Error: processing vignette 'wikisourcer.Rmd' failed with diagnostics:
HTTP error 404.
--- failed re-building ‘wikisourcer.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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  7.3Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
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.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
File ‘wordspace/libs/wordspace.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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  5.8Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
File ‘wskm/libs/wskm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    bin   5.4Mb
installed size is 21.9Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
Running ‘testthat.R’ [69s/56s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(xgboost)
  > 
  > test_check("xgboost")
  OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
  OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  [1]	train-error:0.011055 
  ── 1. Failure: xgb.cv works (@test_basic.R#185)  ───────────────────────────────
  cv$evaluation_log[, min(test_error_std)] is not strictly less than 0.004. Difference: 0.00328
  
  [1]	train-logloss:0.380601 
  [2]	train-logloss:0.247327 
  [3]	train-logloss:0.175046 
  [4]	train-logloss:0.122303 
  [5]	train-logloss:0.089890 
  [1]	train-logloss:0.497351 
  [2]	train-logloss:0.357289 
  [3]	train-logloss:0.257217 
  [4]	train-logloss:0.184524 
  [5]	train-logloss:0.132112 
  [1]	train-auc:0.900000	test-auc:0.800000 
  ── 2. Failure: prediction in early-stopping xgb.cv works (@test_callbacks.R#301)
  abs(err_pred - err_log_last) is not strictly more than 1e-04. Difference: -9.99e-05
  
  [1]	eval-error:0.042831	train-error:0.046522 
  [2]	eval-error:0.021726	train-error:0.022263 
  [1]	eval-error:0.042831	train-error:0.046522 
  [2]	eval-error:0.021726	train-error:0.022263 
  [1]	train-error:0.046522 
  [2]	train-error:0.022263 
  [1]	train-error:0.333333 
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 562 SKIPPED: 4 FAILED: 2
  1. Failure: xgb.cv works (@test_basic.R#185) 
  2. Failure: prediction in early-stopping xgb.cv works (@test_callbacks.R#301) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    java  19.0Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    java   9.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    exampleData   1.6Mb
    examples      4.6Mb
File ‘XMRF/libs/XMRF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘Usingxtractomatic.Rmd’ using rmarkdown
date	lon	lat	lowLon	higLon	lowLat	higLat
4/23/2003	203.899	19.664	203.899	203.899	19.664	19.664
4/24/2003	204.151	19.821	203.912597	204.389403	18.78051934	20.86148066
4/30/2003	203.919	20.351	203.6793669	204.1586331	18.79728188	21.90471812
5/1/2003	204.229	20.305	203.9943343	204.4636657	18.90440013	21.70559987
Quitting from lines 818-843 (Usingxtractomatic.Rmd) 
Error: processing vignette 'Usingxtractomatic.Rmd' failed with diagnostics:
(converted from warning) Removed 4070 rows containing missing values (geom_raster).
--- failed re-building ‘Usingxtractomatic.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
Namespace in Imports field not imported from: ‘ghyp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Amelia’ ‘MatchIt’ ‘WhatIf’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘testthat’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/zonator.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  analyzeFMRI.c:948:3: warning: ‘strncat’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  analyzeFMRI.c:975:5: warning: ‘strncat’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/AnalyzeFMRI.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [19s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(aphid)
  > 
  > test_check("aphid")
  ── 1. Failure: Character and raw inputs give same output (@test_PHMM.R#137)  ───
  round(x.vit$score) not equal to round(xDNA.vit$score).
  1/1 mismatches
  [1] 90 - 91 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 44 SKIPPED: 0 FAILED: 1
  1. Failure: Character and raw inputs give same output (@test_PHMM.R#137) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [28s/81s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(atlantistools)
  > 
  > test_check("atlantistools")
  ── 1. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase
  dim(df1) not equal to c(4, 16).
  1/2 mismatches
  [1] 5 - 4 == 1
  
  ── 2. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase
  df1$linf[3] not equivalent to 87.4.
  1/1 mismatches
  [1] 75.1 - 87.4 == -12.3
  
  ── 3. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase
  df1$k[2] not equivalent to 0.15.
  1/1 mismatches
  [1] 0.53 - 0.15 == 0.38
  
  ── 4. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase
  df1$locality[1] not equivalent to "Central Adriatic, 100-200 m depth".
  1/1 mismatches
  x[1]: "northeast Mediterranean Sea"
  y[1]: "Central Adriatic, 100-200 m depth"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 193 SKIPPED: 1 FAILED: 4
  1. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase.R#6) 
  2. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase.R#7) 
  3. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase.R#8) 
  4. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See ‘/data/gannet/ripley/R/packages/tests-devel/audio.Rcheck/00install.out’ for details.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("bayesCT")
  Loading required package: bayesCT
  
  Attaching package: 'bayesCT'
  
  The following object is masked from 'package:stats':
  
      simulate
  
  ── 1. Failure: The randomization is (@test_randomization.R#8)  ─────────────────
  sum(randomization(12, 10, c(3, 2)) == 1) not equal to 5.
  1/1 mismatches
  [1] 4 - 5 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 41 SKIPPED: 0 FAILED: 1
  1. Failure: The randomization is (@test_randomization.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  mcmc.c:337:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/BayHap.Rcheck/00install.out’ for details.
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
Running ‘testthat.R’ [234s/261s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BMSC)
  Loading required package: Rcpp
  > 
  > test_check("BMSC")
  ── 1. Failure: A message is returned if some rows are missing (@test_missingValu
  `BMSC:::handleMissingData(data, formula, yUncertainty)$data` produced unexpected messages.
  Expected match: 7 rows \\(9.33% of the data\\) were excluded due to missing values.
  Actual values:
  * 8 rows (10.67% of the data) were excluded due to missing values.
  
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 61 SKIPPED: 1 FAILED: 1
  1. Failure: A message is returned if some rows are missing (@test_missingValuesHandling.R#47) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [227s/253s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(brms)
  Loading required package: Rcpp
  Loading required package: ggplot2
  Loading 'brms' package (version 2.7.0). Useful instructions
  can be found by typing help('brms'). A more detailed introduction
  to the package is available through vignette('brms_overview').
  Run theme_set(theme_default()) to use the default bayesplot theme.
  > 
  > test_check("brms")
  ── 1. Failure: first_greater returns expected results (@tests.brmsfit-helpers.R#
  first_greater(A, x) not equal to c(3, 3, 3, 3, 2, 1, 2, 2, 2, 3).
  4/10 mismatches (average diff: 1.5)
  [6]  3 - 1 ==  2
  [7]  1 - 2 == -1
  [8]  3 - 2 ==  1
  [10] 1 - 3 == -2
  
  ── 2. Failure: first_greater returns expected results (@tests.brmsfit-helpers.R#
  first_greater(A, x, i = 2) not equal to c(3, 3, 3, 3, 2, 2, 2, 2, 2, 3).
  3/10 mismatches (average diff: 1)
  [6]  3 - 2 ==  1
  [8]  3 - 2 ==  1
  [10] 2 - 3 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1263 SKIPPED: 4 FAILED: 2
  1. Failure: first_greater returns expected results (@tests.brmsfit-helpers.R#7) 
  2. Failure: first_greater returns expected results (@tests.brmsfit-helpers.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  hash.c:144:5: warning: ‘strncpy’ specified bound 2048 equals destination size [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/C50.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [86s/311s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(caret)
  Loading required package: lattice
  Loading required package: ggplot2
  > 
  > test_check("caret")
  ── 1. Failure: twoClassSummary is calculating correctly (@test_twoClassSummary.R
  mod1$resample$ROC not equal to mod2$resample$ROC.
  2/25 mismatches (average diff: 0.0045)
  [18] 0.836 - 0.831 ==  0.00529
  [21] 0.537 - 0.541 == -0.00370
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 105 SKIPPED: 32 FAILED: 1
  1. Failure: twoClassSummary is calculating correctly (@test_twoClassSummary.R#31) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  catnet_rexport.cpp:202:17: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:206:15: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:213:16: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
  catnet_rexport.cpp:216:18: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:217:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:232:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:231:18: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/catnet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  MLEEstimator.cpp:81:17: warning: catching polymorphic type ‘class std::domain_error’ by value [-Wcatch-value=]
  MLEEstimator.cpp:127:17: warning: catching polymorphic type ‘class std::domain_error’ by value [-Wcatch-value=]
See ‘/data/gannet/ripley/R/packages/tests-devel/catSurv.Rcheck/00install.out’ for details.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(clhs)
  > 
  > test_check("clhs")
  ── 1. Failure: basic clhs on a data.frame works (@test-clhs-data.frame.R#15)  ──
  `res` not equal to c(188, 657, 140, 301, 817).
  5/5 mismatches (average diff: 210)
  [1]  97 - 188 == -91
  [2] 903 - 657 == 246
  [3] 539 - 140 == 399
  [4] 451 - 301 == 150
  [5] 979 - 817 == 162
  
  ── 2. Failure: DLHS method on a data.frame works (@test-method_DLHS.R#17)  ─────
  `res` not equal to c(214, 40, 702, 919, 521).
  5/5 mismatches (average diff: 211)
  [1] 412 - 214 ==  198
  [2] 170 -  40 ==  130
  [3] 196 - 702 == -506
  [4] 820 - 919 ==  -99
  [5] 641 - 521 ==  120
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 4 SKIPPED: 0 FAILED: 2
  1. Failure: basic clhs on a data.frame works (@test-clhs-data.frame.R#15) 
  2. Failure: DLHS method on a data.frame works (@test-method_DLHS.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  hash.c:144:5: warning: ‘strncpy’ specified bound 2048 equals destination size [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/Cubist.Rcheck/00install.out’ for details.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(cusum)
  > 
  > test_check("cusum")
  ── 1. Failure: Output of Control limit simulation (@test-racusum.R#21)  ────────
  `result` not equal to `expected_results`.
  4/10 mismatches (average diff: 0.893)
  [7]  0.00 - 0.51 == -0.51
  [8]  0.00 - 1.02 == -1.02
  [9]  0.60 - 1.53 == -0.93
  [10] 0.42 - 1.53 == -1.11
  
  ── 2. Failure: Output of alpha simulation (@test-racusum_alpha_sim.R#20)  ──────
  `works` not equal to `expected_results`.
  1/1 mismatches
  [1] 0.023 - 0.025 == -0.002
  
  ── 3. Failure: Output of Control limit simulation (@test_racusum_limit_sim.R#19)
  `works` not equal to `expected_results`.
  1/1 mismatches
  [1] 2.45 - 2.59 == -0.14
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 3 SKIPPED: 0 FAILED: 3
  1. Failure: Output of Control limit simulation (@test-racusum.R#21) 
  2. Failure: Output of alpha simulation (@test-racusum_alpha_sim.R#20) 
  3. Failure: Output of Control limit simulation (@test_racusum_limit_sim.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [43s/86s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DataExplorer)
  > 
  > test_check("DataExplorer")
  ── 1. Failure: .ignoreCat (@test-internal.r#11)  ───────────────────────────────
  as.numeric(.ignoreCat(dt, 0)) not equal to c(1L, 2L, 5L, 10L).
  1/4 mismatches
  [3] 4 - 5 == -1
  
  ── 2. Failure: .ignoreCat (@test-internal.r#12)  ───────────────────────────────
  as.numeric(.ignoreCat(dt, 1)) not equal to c(2L, 5L, 10L).
  1/3 mismatches
  [2] 4 - 5 == -1
  
  ── 3. Failure: .ignoreCat (@test-internal.r#13)  ───────────────────────────────
  as.numeric(.ignoreCat(dt, 2)) not equal to c(5L, 10L).
  1/2 mismatches
  [1] 4 - 5 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 130 SKIPPED: 7 FAILED: 3
  1. Failure: .ignoreCat (@test-internal.r#11) 
  2. Failure: .ignoreCat (@test-internal.r#12) 
  3. Failure: .ignoreCat (@test-internal.r#13) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘degenes-Ex.R’ failed
The error most likely occurred in:

> ### Name: deg
> ### Title: Detection of differentially expressed genes.
> ### Aliases: deg
> 
> ### ** Examples
> 
> X1 = matrix(rnorm(2000, 0, 1), 200, 10)
> X2 = matrix(rnorm(2000, 0, 1), 200, 10)
> index = sample(1:200, 5, replace=FALSE)
> X2[index,] = X2[index,] + 5
> D = deg(X1, X2)
Sun Mar  3 18:39:34 2019
Calculation of Z
Calculation of z
Calculation of the kernel estimator
Calculation of the kernel estimator
Determination of the rejection region
Error in if (integral > single.alpha) c1 <- c : 
  missing value where TRUE/FALSE needed
Calls: deg
Execution halted
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/Delaporte.Rcheck/00install.out’ for details.
Found the following significant warnings:
  GetData.c:342:15: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 3 [-Wformat-overflow=]
  GetData.c:355:15: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 3 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/DetSel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  clipper.cpp:721:34: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct ClipperLib::TEdge’; use assignment or value-initialization instead [-Wclass-memaccess]
  dbfopen.c:1346:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:1328:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:879:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopen.c:1693:9: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
  dbfopen.c:2065:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/dggridR.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [14s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(disclapmix)
  > 
  > test_check("disclapmix")
  ── 1. Failure: simulate (@test-disclapmix.R#152)  ──────────────────────────────
  sim_fit$disclap_parameters not equal to fit_std_int_coef$disclap_parameters.
  5/6 mismatches (average diff: 0.139)
  [1] 0.326 - 0.453 == -0.127
  [2] 0.454 - 0.311 ==  0.142
  [4] 0.337 - 0.224 ==  0.113
  [5] 0.364 - 0.540 == -0.176
  [6] 0.506 - 0.371 ==  0.135
  
  ── 2. Failure: simulate (@test-disclapmix.R#153)  ──────────────────────────────
  sim_fit$y not equal to fit_std_int_coef$y.
  4/6 mismatches (average diff: 1.5)
  [3] 20 - 19 ==  1
  [4] 19 - 20 == -1
  [5] 22 - 20 ==  2
  [6] 20 - 22 == -2
  
  ── 3. Failure: rcpp_find_haplotype_in_matrix (@test-disclapmix.R#209)  ─────────
  33 not equal to find_haplotype_in_matrix(x, x[33L, ]).
  1/1 mismatches
  [1] 33 - 1 == 32
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 50 SKIPPED: 0 FAILED: 3
  1. Failure: simulate (@test-disclapmix.R#152) 
  2. Failure: simulate (@test-disclapmix.R#153) 
  3. Failure: rcpp_find_haplotype_in_matrix (@test-disclapmix.R#209) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/distrEllipse.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/dpglasso.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [194s/246s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(dtwclust)
  Loading required package: proxy
  
  Attaching package: 'proxy'
  
  The following objects are masked from 'package:stats':
  
      as.dist, dist
  
  The following object is masked from 'package:base':
  
      as.matrix
  
  Loading required package: dtw
  Loaded dtw v1.20-1. See ?dtw for help, citation("dtw") for use in publication.
  
  dtwclust:
  Setting random number generator to L'Ecuyer-CMRG (see RNGkind()).
  To read the included vignettes type: browseVignettes("dtwclust").
  See news(package = "dtwclust") after package updates.
  > library(foreach)
  > library(testthat)
  > 
  > # coverage for multi-threading might not be possible (?)
  > if (nzchar(Sys.getenv("R_COVR"))) RcppParallel::setThreadOptions(1L)
  > # old reporter for CMD checks
  > options(testthat.default_reporter = "summary")
  > 
  > #' To test in a local machine:
  > #' Sys.setenv(NOT_CRAN = "true"); test_dir("tests/testthat/")
  > #' OR
  > #' devtools::test() # broken, can't figure out why
  > #'
  > #' To disable parallel tests, before calling test() run:
  > #'
  > #'   options(dtwclust_skip_par_tests = TRUE)
  > #'
  > testthat::test_check("dtwclust")
  ── 1. Failure: Cluster reinitialization in partitional tsclust works.  ─────────
  `... <- NULL` did not produce any warnings.
  
  ── 2. Failure: Cluster reinitialization in partitional tsclust works.  ─────────
  pc_cr@converged isn't false.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1889 SKIPPED: 3 FAILED: 2
  1. Failure: Cluster reinitialization in partitional tsclust works. 
  2. Failure: Cluster reinitialization in partitional tsclust works. 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(edfReader)
  > 
  > test_check("edfReader")
  edfPlusC.edf : Testing header
  edfPlusC.edf : Testing signals
  bdfPlusC.bdf : Testing header
  bdfPlusC.bdf : Testing signals
  edfAnnonC.edf : Testing header
  edfAnnonC.edf : Testing signals
  edfPlusD.edf : Testing header
  edfPlusD.edf : Testing signals
  testASignalsFile edfPlusC.edf 
  testASignalsFile bdfPlusC.bdf 
  testASignalsFile edfPlusD.edf 
  testASignalsFile edfAnnonC.edf 
  ── 1. Failure: A6: A random range 3 (@test20_FromTill.R#162)  ──────────────────
  aSignal$annotations not equal to allAnnots[annotsInRange, ].
  Attributes: < Component "row.names": Mean relative difference: 0.6666667 >
  
  edfPlusC.edf : testOSignalsFile: isContinuous= TRUE 
  bdfPlusC.bdf : testOSignalsFile: isContinuous= TRUE 
  edfPlusD.edf : testOSignalsFile: isContinuous= FALSE 
  edfAnnonC.edf : testOSignalsFile: isContinuous= TRUE 
  edfPlusC.edf : min/max tests
  bdfPlusC.bdf : min/max tests
  edfPlusD.edf : min/max tests
  edfAnnonC.edf : min/max tests
  edfPlusC.edf : signal selection tests
  bdfPlusC.bdf : signal selection tests
  edfPlusD.edf : signal selection tests
  edfAnnonC.edf : signal selection tests
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 790 SKIPPED: 0 FAILED: 1
  1. Failure: A6: A random range 3 (@test20_FromTill.R#162) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘test-all.R’ [13s/13s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(eeptools)
  Loading required package: ggplot2
  > 
  > test_check("eeptools")
  ── 1. Failure: statamode returns correct modes for each method using numbers (@t
  `d` not equal to 4.
  1/1 mismatches
  [1] 7 - 4 == 3
  
  ── 2. Failure: statamode handles all types of modes (@test-statamode.r#128)  ───
  statamode(vecA, method = tests[i, "method"]) not equal to "B".
  1/1 mismatches
  x[1]: "F"
  y[1]: "B"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 517 SKIPPED: 0 FAILED: 2
  1. Failure: statamode returns correct modes for each method using numbers (@test-statamode.r#24) 
  2. Failure: statamode handles all types of modes (@test-statamode.r#128) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [17s/70s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (packageVersion("testthat") >= "0.9.1") {
  +   library(testthat)
  +   test_check("emil")
  + }
  Loading required package: emil
  
  Attaching package: 'emil'
  
  The following object is masked from 'package:base':
  
      mode
  
  ── 1. Failure: k-NN imputation (@test-preprocess.r#30)  ────────────────────────
  sets$test$x[na.ind] not equivalent to ifelse(na.ind[, 2] <= 3, 5, 4.5).
  3/10 mismatches (average diff: 0.5)
  [5]  5 - 4.5 == 0.5
  [7]  5 - 4.5 == 0.5
  [10] 5 - 4.5 == 0.5
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 183 SKIPPED: 1 FAILED: 1
  1. Failure: k-NN imputation (@test-preprocess.r#30) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  main.c:334:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:575:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:518:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:805:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:755:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1034:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:983:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1377:7: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1279:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1678:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1962:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1912:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:2316:7: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:2212:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/enviPat.Rcheck/00install.out’ for details.
Found the following significant warnings:
  epanet.c:999:5: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:1000:5: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:1492:3: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:2308:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:2309:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input1.c:454:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input1.c:455:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input3.c:604:2: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/epanet2toolkit.Rcheck/00install.out’ for details.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fabricatr)
  > 
  > test_check("fabricatr")
  ── 1. Failure: Multi-level Resample validity (@test-resampling.R#155)  ─────────
  length(unique(split(resample_validity$cities, rep(1:6, each = 5)))) not equal to 6.
  1/1 mismatches
  [1] 5 - 6 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 363 SKIPPED: 1 FAILED: 1
  1. Failure: Multi-level Resample validity (@test-resampling.R#155) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/data/gannet/ripley/R/packages/tests-devel/FastRWeb.Rcheck/00install.out’ for details.
Found the following significant warnings:
  gropt/src/SmartSpace.cpp:142:24: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
See ‘/data/gannet/ripley/R/packages/tests-devel/fdasrvf.Rcheck/00install.out’ for details.
Found the following significant warnings:
  RngStream.c:275:7: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/freeknotsplines.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [12s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(funData)
  
  Attaching package: 'funData'
  
  The following object is masked from 'package:stats':
  
      integrate
  
  > 
  > test_check("funData")
  ── 1. Failure: sparsify (@test_simulation.R#219)  ──────────────────────────────
  nObsPoints(s) not equal to c(2, 2).
  1/2 mismatches
  [2] 3 - 2 == 1
  
  ── 2. Failure: sparsify (@test_simulation.R#220)  ──────────────────────────────
  argvals(s) not equal to list(c(0.57, 0.7), c(0.94, 0.95)).
  Component 1: Mean relative difference: 0.1360544
  Component 2: Numeric: lengths (3, 2) differ
  
  ── 3. Failure: sparsify (@test_simulation.R#221)  ──────────────────────────────
  X(s) not equal to list(c(1.17678, -2.76915), c(-2.40195, -2.32616)).
  Component 1: Mean relative difference: 0.7422477
  Component 2: Numeric: lengths (3, 2) differ
  
  ── 4. Failure: sparsify (@test_simulation.R#227)  ──────────────────────────────
  as.irregFunData(s[[1]])@argvals not equal to list(4, 2).
  Component 1: Mean relative difference: 1
  Component 2: Numeric: lengths (2, 1) differ
  
  ── 5. Failure: sparsify (@test_simulation.R#228)  ──────────────────────────────
  as.irregFunData(s[[1]])@X not equal to list(4, 3).
  Component 1: Mean relative difference: 1
  Component 2: Numeric: lengths (2, 1) differ
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 488 SKIPPED: 0 FAILED: 5
  1. Failure: sparsify (@test_simulation.R#219) 
  2. Failure: sparsify (@test_simulation.R#220) 
  3. Failure: sparsify (@test_simulation.R#221) 
  4. Failure: sparsify (@test_simulation.R#227) 
  5. Failure: sparsify (@test_simulation.R#228) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  hap_c.c:380:28: warning: ‘%03d’ directive writing between 3 and 10 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  hap_c.c:392:28: warning: ‘%03d’ directive writing between 3 and 10 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/gap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Gdmlib.cpp:2352:19: warning: ‘%lf’ directive writing between 3 and 317 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/gdm.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [76s/86s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check('ggfortify')
  Loading required package: ggfortify
  Loading required package: ggplot2
  initial  value 7.505733 
  final  value 7.505688 
  converged
  Initial stress        : 0.01705
  stress after  10 iters: 0.00951, magic = 0.500
  stress after  20 iters: 0.00941, magic = 0.500
  initial  value 7.505733 
  final  value 7.505688 
  converged
  Initial stress        : 0.01705
  stress after  10 iters: 0.00951, magic = 0.500
  stress after  20 iters: 0.00941, magic = 0.500
  ── 1. Failure: fortify.glmnet works for Orange (@test-glmnet.R#33)  ────────────
  dim(fortified) not equal to c(57, 5).
  1/2 mismatches
  [1] 56 - 57 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1451 SKIPPED: 9 FAILED: 1
  1. Failure: fortify.glmnet works for Orange (@test-glmnet.R#33) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: ‘__var_41_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/gglasso.Rcheck/00install.out’ for details.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/glmmfields.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [46s/51s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > library("GMCM")
  > 
  > test_check("GMCM")
  ── 1. Error: EMAlgorithm returns properly formatted output (@test-EMAlgorithm.R#
  Delta likelihood was negative. Something went wrong!
  1: suppressWarnings({
         res <- GMCM:::EMAlgorithm(dat$z, m = m, max.ite = 100, trace.theta = trace_theta)
     }) at testthat/test-EMAlgorithm.R:12
  2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  3: GMCM:::EMAlgorithm(dat$z, m = m, max.ite = 100, trace.theta = trace_theta) at testthat/test-EMAlgorithm.R:13
  4: stop("Delta likelihood was negative. Something went wrong!") at /data/gannet/ripley/R/packages/tests-devel/GMCM/R/EMAlgortihm.R:88
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2172 SKIPPED: 2 FAILED: 1
  1. Error: EMAlgorithm returns properly formatted output (@test-EMAlgorithm.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Running ‘testthat.R’ [28s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(harvestr)
  > foreach::registerDoSEQ()
  > test_check("harvestr")
  ── 1. Failure: caching in reap with long sample (@test-caching.R#76)  ──────────
  all(t2[1] <= t1[1]) isn't true.
  
  ── 2. Failure: gather gives the appropriate kinds of seed. (@test-gather.R#42)  
  RNGkind() not identical to c("L'Ecuyer-CMRG", "Inversion").
  Lengths differ: 3 is not 2
  
  ── 3. Failure: gather replaces seed. (@test-gather.R#57)  ──────────────────────
  RNGkind() not identical to c("Mersenne-Twister", "Box-Muller").
  Lengths differ: 3 is not 2
  
  ── 4. Failure: get.seed retrieves properly (@test-seeds.R#14)  ─────────────────
  `seed` not identical to `eseed`.
  Mean relative difference: 0.9608917
  
  ── 5. Failure: replace.seed (@test-seeds.R#29)  ────────────────────────────────
  `k` not identical to c("Mersenne-Twister", "Box-Muller").
  Lengths differ: 3 is not 2
  
  ── 6. Failure: replace.seed (@test-seeds.R#30)  ────────────────────────────────
  `l` not identical to c("L'Ecuyer-CMRG", "Inversion").
  Lengths differ: 3 is not 2
  
  ── 7. Failure: withseed replaces previous seed. (@test-seeds.R#56)  ────────────
  RNGkind() not identical to c("Mersenne-Twister", "Box-Muller").
  Lengths differ: 3 is not 2
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 118 SKIPPED: 5 FAILED: 7
  1. Failure: caching in reap with long sample (@test-caching.R#76) 
  2. Failure: gather gives the appropriate kinds of seed. (@test-gather.R#42) 
  3. Failure: gather replaces seed. (@test-gather.R#57) 
  4. Failure: get.seed retrieves properly (@test-seeds.R#14) 
  5. Failure: replace.seed (@test-seeds.R#29) 
  6. Failure: replace.seed (@test-seeds.R#30) 
  7. Failure: withseed replaces previous seed. (@test-seeds.R#56) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  readstat/readstat_writer.c:82:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  readstat/readstat_writer.c:276:5: warning: ‘strncpy’ specified bound 256 equals destination size [-Wstringop-truncation]
  readstat/readstat_writer.c:331:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  readstat/sas/readstat_sas7bcat_write.c:108:5: warning: ‘strncpy’ output may be truncated copying 64 bytes from a string of length 99 [-Wstringop-truncation]
  readstat/sas/readstat_sas.c:284:5: warning: ‘strncpy’ output may be truncated copying 64 bytes from a string of length 99 [-Wstringop-truncation]
  readstat/sas/readstat_sas.c:337:5: warning: ‘strncpy’ output may be truncated copying 8 bytes from a string of length 31 [-Wstringop-truncation]
  readstat/spss/readstat_sav_write.c:156:5: warning: ‘strncpy’ output may be truncated copying 9 bytes from a string of length 9 [-Wstringop-truncation]
  readstat/spss/readstat_sav_write.c:164:5: warning: ‘strncpy’ output may be truncated copying 8 bytes from a string of length 8 [-Wstringop-truncation]
  readstat/spss/readstat_por_write.c:205:5: warning: ‘strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/haven.Rcheck/00install.out’ for details.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(hdme)
  > 
  > test_check("hdme")
  ── 1. Failure: cv_corrected_lasso computes correctly (@test_corrected_lasso.R#27
  round(cv_fit$loss_min, 2) not equal to round(1.13, 2).
  1/1 mismatches
  [1] 0.98 - 1.13 == -0.15
  
  ── 2. Failure: cv_corrected_lasso computes correctly (@test_corrected_lasso.R#28
  round(cv_fit$radius_1se, 2) not equal to round(1.1, 2).
  1/1 mismatches
  [1] 2.19 - 1.1 == 1.09
  
  ── 3. Failure: cv_corrected_lasso computes correctly (@test_corrected_lasso.R#29
  round(cv_fit$loss_1se, 2) not equal to round(1.52, 2).
  1/1 mismatches
  [1] 0.98 - 1.52 == -0.54
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 9 SKIPPED: 0 FAILED: 3
  1. Failure: cv_corrected_lasso computes correctly (@test_corrected_lasso.R#27) 
  2. Failure: cv_corrected_lasso computes correctly (@test_corrected_lasso.R#28) 
  3. Failure: cv_corrected_lasso computes correctly (@test_corrected_lasso.R#29) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  gener.c:39:26: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/hier.part.Rcheck/00install.out’ for details.
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.
Running ‘testthat.R’ [12s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(hutils)
  > 
  > test_check("hutils")
  ── 1. Failure: Mutate other weighted with mass (@test_1-0-0_mutate_other.R#206) 
  uniqueN(routes_pax_othered[["dest"]]) not equal to 7.
  1/1 mismatches
  [1] 6 - 7 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 591 SKIPPED: 14 FAILED: 1
  1. Failure: Mutate other weighted with mass (@test_1-0-0_mutate_other.R#206) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘IBDsim-Ex.R’ failed
The error most likely occurred in:

> ### Name: oneLocusIBD
> ### Title: Estimating pairwise IBD coefficients
> ### Aliases: oneLocusIBD
> ### Keywords: math
> 
> ### ** Examples
> 
> ### Example 1: Full siblings
> x <- nuclearPed(2) 
> Nsim <- 100 # Should be increased substantially
> 
> # Autosomal kappa: Estimate vs exact 
> k_est = oneLocusIBD(x, ind1=3, ind2=4, Nsim=Nsim, seed=123)
---------------
Performing unconditional simulation
Mode: autosomal 
Recombination model: haldane (poisson process) 
Number of simulations: 100 
Simulation finished. Time used: 0.047 seconds
---------------
IBD analysis finished. Total time used: 0.051 seconds.
> k_exact = c(0.25, 0.5, 0.25)
> stopifnot(all(round(k_est - k_exact, 1) == 0))
Error: all(round(k_est - k_exact, 1) == 0) is not TRUE
Execution halted
Running ‘testthat.R’ [14s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(infer)
  > 
  > test_check("infer")
  Setting `type = "permute"` in `generate()`.
  ── 1. Failure: conf_int argument works (@test-wrappers.R#141)  ─────────────────
  no_var_equal == var_equal isn't false.
  
  ── 2. Failure: conf_int argument works (@test-wrappers.R#153)  ─────────────────
  shortcut_no_var_equal == shortcut_var_equal isn't false.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 347 SKIPPED: 0 FAILED: 2
  1. Failure: conf_int argument works (@test-wrappers.R#141) 
  2. Failure: conf_int argument works (@test-wrappers.R#153) 
  
  Error: testthat unit tests failed
  Execution halted
Interpol: no visible global function definition for ‘splinefun’
Undefined global functions or variables:
  splinefun
Consider adding
  importFrom("stats", "splinefun")
to your NAMESPACE file.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(janitor)
  > 
  > test_check("janitor")
  ── 1. Failure: users can supply own Ns (@test-adorn-ns.R#129)  ─────────────────
  `%>%`(...) not equal to data.frame(...).
  Component "big": 2 string mismatches
  Component "small": 2 string mismatches
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 438 SKIPPED: 0 FAILED: 1
  1. Failure: users can supply own Ns (@test-adorn-ns.R#129) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [28s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(jpmesh)
  > 
  > test_check("jpmesh")
  ── 1. Failure: Generate random meshcode (@test-rmesh.R#8)  ─────────────────────
  `res` not equal to "50304610".
  1/1 mismatches
  x[1]: "64394175"
  y[1]: "50304610"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 133 SKIPPED: 0 FAILED: 1
  1. Failure: Generate random meshcode (@test-rmesh.R#8) 
  
  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.
Found the following significant warnings:
  /data/gannet/ripley/R/test-3.6/BH/include/boost/container/detail/copy_move_algo.hpp:183:19: 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-3.6/BH/include/boost/container/detail/copy_move_algo.hpp:897:16: 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-3.6/BH/include/boost/container/detail/copy_move_algo.hpp:197:19: 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.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lolR)
  > 
  > test_check("lolR")
  ── 1. Failure: Optimal Embedding Dimensions (@test-xval.R#45)  ─────────────────
  result.rs$optimal.lhat not equal to result.rs.noset$optimal.lhat.
  Lengths differ: 2 is not 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 446 SKIPPED: 0 FAILED: 1
  1. Failure: Optimal Embedding Dimensions (@test-xval.R#45) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [15s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(loo)
  This is loo version 2.0.0.
  **NOTE: As of version 2.0.0 loo defaults to 1 core but we recommend using as many as possible. Use the 'cores' argument or set options(mc.cores = NUM_CORES) for an entire session. Visit mc-stan.org/loo/news for details on other changes.
  
  Attaching package: 'loo'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  > Sys.setenv("R_TESTS" = "")
  > test_check("loo")
  ── 1. Failure: weighted quantiles work (@test_E_loo.R#155)  ────────────────────
  .wquant(x1, w1, pr) not equal to .wquant_sim(x1, w1, pr, n_sim = 2e+06).
  35/39 mismatches (average diff: 0.012)
  [1]  -2.005 - -1.987 == -0.01808
  [2]  -1.688 - -1.647 == -0.04073
  [3]  -1.472 - -1.440 == -0.03245
  [4]  -1.269 - -1.280 ==  0.01101
  [5]  -1.143 - -1.152 ==  0.00863
  [6]  -1.040 - -1.042 ==  0.00202
  [7]  -0.946 - -0.943 == -0.00287
  [8]  -0.831 - -0.837 ==  0.00630
  [10] -0.658 - -0.667 ==  0.00869
  ...
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 378 SKIPPED: 0 FAILED: 1
  1. Failure: weighted quantiles work (@test_E_loo.R#155) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Manifolds/SmartSpace.cpp:147:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
See ‘/data/gannet/ripley/R/packages/tests-devel/ManifoldOptim.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [23s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(matrixTests)
  > 
  > test_check("matrixTests")
  ── 1. Failure: monte-carlo random testing gives equal results (@test-correct-cor
  `t1` not equal to `t2`.
  Component "conf.level": Mean absolute difference: 0.2742743
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 836 SKIPPED: 0 FAILED: 1
  1. Failure: monte-carlo random testing gives equal results (@test-correct-cor_pearson.R#58) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [64s/119s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(metR)
  > library(vdiffr)
  > 
  > test_check("metR")
  ── 1. Failure: EOF changes probs (@test_eof.R#21)  ─────────────────────────────
  {
      ...
  } not identical to 1524903.
  1/1 mismatches
  [1] 1523828 - 1524903 == -1075
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 62 SKIPPED: 16 FAILED: 1
  1. Failure: EOF changes probs (@test_eof.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [70s/106s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mice)
  Loading required package: lattice
  
  Attaching package: 'mice'
  
  The following objects are masked from 'package:base':
  
      cbind, rbind
  
  > 
  > test_check("mice")
  ── 1. Failure: retains same numerical result (@test-pool.R#13)  ────────────────
  unname(getqbar(est)) not equal to `mn`.
  5/5 mismatches (average diff: 0.895)
  [1] 19.7878 - 18.7617 ==  1.02603
  [2]  0.0513 -  0.0536 == -0.00229
  [3] -6.1563 - -4.5737 == -1.58260
  [4] -7.7136 - -6.6360 == -1.07766
  [5]  2.9521 -  2.1636 ==  0.78847
  
  ── 2. Failure: retains same numerical result (@test-pool.R#14)  ────────────────
  unname(summary(est)[, "std.error"]) not equal to `se`.
  5/5 mismatches (average diff: 0.329)
  [1] 3.4259 - 4.0028 == -0.57694
  [2] 0.0187 - 0.0224 == -0.00363
  [3] 1.6195 - 2.0340 == -0.41452
  [4] 1.9746 - 2.4598 == -0.48513
  [5] 1.8642 - 2.0290 == -0.16475
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 274 SKIPPED: 0 FAILED: 2
  1. Failure: retains same numerical result (@test-pool.R#13) 
  2. Failure: retains same numerical result (@test-pool.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [24s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > #library(microsamplingDesign)
  > 
  > #source("generateTestData.R")
  > 
  > #test_check("microsamplingDesign")
  > 
  > testthat::test_check("microsamplingDesign")
  Loading required package: microsamplingDesign
  start Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  2 cores── 1. Failure: Equal ranking timePoints (@testRankTimePoints.R#43)  ────────────
  rankTimePointsOrig@ranking not equal to rankedTimePointsNew@ranking.
  Component "name": 7 string mismatches
  Component "criterion": Mean relative difference: 0.04047401
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 21 SKIPPED: 3 FAILED: 1
  1. Failure: Equal ranking timePoints (@testRankTimePoints.R#43) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  migrate.c:179:30: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:186:26: warning: ‘.asc’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:199:28: warning: ‘.asc’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:286:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:312:29: warning: ‘%d’ directive writing between 1 and 8 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:559:31: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:595:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:603:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/MigClim.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘ade4’ ‘softImpute’
  All declared Imports should be used.
listGenoToTable: no visible binding for global variable ‘dummy’
Undefined global functions or variables:
  dummy
Found the following significant warnings:
  monetdblite/src/gdk/gdk_heap.c:189:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
  monetdblite/src/gdk/gdk_heap.c:260:30: warning: ‘%s’ directive writing likely 3 or more bytes into a region of size between 0 and 99 [-Wformat-overflow=]
  monetdblite/src/mal/sqlbackend/rel_bin.c:2949:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/rel_bin.c:1083:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/sql_statement.c:3193:3: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/sql_statement.c:3196:3: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/sql_statement.c:3186:3: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/sql/server/rel_planner.c:82:4: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/sql/server/rel_semantic.c:54:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/sql/server/rel_updates.c:1729:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/MonetDBLite.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [59s/75s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > # Sys.setenv("MONETDBLITE_INMEMORY" = "yes")
  > # test_check("MonetDBLite")
  > Sys.setenv("MONETDBLITE_INMEMORY" = "no")
  > test_check("MonetDBLite")
  Loading required package: MonetDBLite
  ── 1. Failure: db allows svyby commands (@test_05_survey.R#60)  ────────────────
  round(...) not equal to 0.022.
  1/1 mismatches
  [1] 0.019 - 0.022 == -0.003
  
  ── 2. Failure: db allows svyby commands (@test_05_survey.R#62)  ────────────────
  ...[] not equal to 10.11.
  1/1 mismatches
  [1] 10.3 - 10.1 == 0.23
  
  [1] "E"
  [1] "H"
  [1] "M"
  ── 3. Failure: db allows svyby commands (@test_05_survey.R#66)  ────────────────
  round(SE(a)[2], 2) not equal to 4708.41.
  1/1 mismatches
  [1] 5476 - 4708 == 768
  
  ── 4. Failure: db allows svyby commands (@test_05_survey.R#67)  ────────────────
  as.numeric(round(cv(a)[2], 4)) not equal to 0.2975.
  1/1 mismatches
  [1] 0.346 - 0.297 == 0.0486
  
  ── 5. Failure: db allows svyby commands (@test_05_survey.R#69)  ────────────────
  round(confint(a, df = degf(rclus1))[2, 2], 2) not equal to 30808.26.
  1/1 mismatches
  [1] 33252 - 30808 == 2443
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 315 SKIPPED: 13 FAILED: 5
  1. Failure: db allows svyby commands (@test_05_survey.R#60) 
  2. Failure: db allows svyby commands (@test_05_survey.R#62) 
  3. Failure: db allows svyby commands (@test_05_survey.R#66) 
  4. Failure: db allows svyby commands (@test_05_survey.R#67) 
  5. Failure: db allows svyby commands (@test_05_survey.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘test_base.R’ [60s/68s]
Running the tests in ‘tests/test_base.R’ failed.
Complete output:
  > library(testthat)
  > test_check("msm")
  Loading required package: msm
  ── 1. Failure: Information matrix (@test_deriv.r#138)  ─────────────────────────
  c(0.88475550512612, 0.202501688704573, -0.474183198550202) not equal to tm$paramdata$info[1:3].
  3/3 mismatches (average diff: 0.284)
  [1]  0.885 -  1.0455 == -0.161
  [2]  0.203 -  0.0872 ==  0.115
  [3] -0.474 - -1.0490 ==  0.575
  
  ── 2. Failure: piecewise constant intensities with pci, with other covariates (@
  448.1228 not equal to cav5cov.msm$minus2loglik.
  1/1 mismatches
  [1] 448 - 456 == -7.79
  
  ── 3. Failure: piecewise constant intensities with pci, with other covariates (@
  448.1228 not equal to cav5cov.msm$minus2loglik.
  1/1 mismatches
  [1] 448 - 456 == -7.79
  
  ── 4. Failure: piecewise constant intensities with pci, with uncentered covariat
  449.692 not equal to cav5cov.msm$minus2loglik.
  1/1 mismatches
  [1] 450 - 458 == -7.82
  
  ── 5. Failure: piecewise constant intensities with pci, with uncentered covariat
  449.692 not equal to cav5cov.msm$minus2loglik.
  1/1 mismatches
  [1] 450 - 458 == -7.82
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 462 SKIPPED: 2 FAILED: 5
  1. Failure: Information matrix (@test_deriv.r#138) 
  2. Failure: piecewise constant intensities with pci, with other covariates (@test_models.r#202) 
  3. Failure: piecewise constant intensities with pci, with other covariates (@test_models.r#210) 
  4. Failure: piecewise constant intensities with pci, with uncentered covariates (@test_models.r#218) 
  5. Failure: piecewise constant intensities with pci, with uncentered covariates (@test_models.r#226) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [66s/72s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(myTAI)
  > 
  > test_check("myTAI")
  
  
  
  ── 1. Failure: PlotEnrichment() computes correct values... (@test-PlotEnrichment
  round(...) not equal to round(c(1, 1, 0.2406024, 1, 1, 0.4215795, 1), 5).
  5/7 mismatches (average diff: 0.519)
  [1] 0.525 - 1.000 == -0.475
  [3] 0.553 - 0.241 ==  0.313
  [5] 0.350 - 1.000 == -0.650
  [6] 1.000 - 0.422 ==  0.578
  [7] 0.422 - 1.000 == -0.578
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 265 SKIPPED: 1 FAILED: 1
  1. Failure: PlotEnrichment() computes correct values... (@test-PlotEnrichment.R#271) 
  
  Error: testthat unit tests failed
  Execution halted
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 significant warnings:
  connection.cpp:67:36: warning: catching polymorphic type ‘class nanodbc::database_error’ by value [-Wcatch-value=]
  odbc_connection.cpp:37:36: warning: catching polymorphic type ‘class nanodbc::database_error’ by value [-Wcatch-value=]
  odbc_connection.cpp:75:36: warning: catching polymorphic type ‘class nanodbc::database_error’ by value [-Wcatch-value=]
See ‘/data/gannet/ripley/R/packages/tests-devel/odbc.Rcheck/00install.out’ for details.
mapvar: no visible global function definition for ‘data’
mapvar: no visible binding for global variable ‘state.fips’
mapvar: no visible global function definition for ‘rgb’
mapvar: no visible global function definition for ‘rect’
mapvar: no visible global function definition for ‘text’
rowScrape: no visible global function definition for ‘tail’
rowScrape: no visible global function definition for ‘head’
scrapeTable: no visible binding for global variable ‘tail’
Undefined global functions or variables:
  data head rect rgb state.fips tail text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "rect", "text")
  importFrom("utils", "data", "head", "tail")
to your NAMESPACE file.
Found the following significant warnings:
  opus_miner.cpp:90:15: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
See ‘/data/gannet/ripley/R/packages/tests-devel/opusminer.Rcheck/00install.out’ for details.
Running ‘anova.R’
  Running ‘clm.fit.R’
  Running ‘clm.formula.R’
  Running ‘clmm.R’ [9s/10s]
  Running ‘clmm.control.R’
  Running ‘clmm.formula.R’
  Running ‘confint.R’
  Running ‘nominal.test.R’
  Running ‘test-all.R’ [27s/29s]
  Running ‘test.clm.Theta.R’
  Running ‘test.clm.convergence.R’
  Running ‘test.clm.flex.link.R’
  Running ‘test.clm.model.matrix.R’
  Running ‘test.clm.predict.R’
  Running ‘test.clm.profile.R’
  Running ‘test.clm.single.anova.R’
  Running ‘test.general.R’
  Running ‘test.makeThresholds.R’
  Running ‘test.sign.R’
  Running ‘test0weights.R’
  Running ‘testAnova.clm2.R’
  Running ‘testCLM.R’
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > 
  > if(require(testthat) && require(ordinal)) {
  +     test_check("ordinal")
  + }
  Loading required package: testthat
  Loading required package: ordinal
  ── 1. Failure: clm gives contrast warnings when it should (@test-contrasts.R#11)
  givesWarnings(...) isn't false.
  
  ── 2. Failure: clm gives contrast warnings when it should (@test-contrasts.R#15)
  givesWarnings(...) isn't false.
  
  ── 3. Failure: clm gives contrast warnings when it should (@test-contrasts.R#19)
  givesWarnings(...) isn't false.
  
  ── 4. Failure: clm gives contrast warnings when it should (@test-contrasts.R#23)
  givesWarnings(...) isn't false.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 80 SKIPPED: 0 FAILED: 4
  1. Failure: clm gives contrast warnings when it should (@test-contrasts.R#11) 
  2. Failure: clm gives contrast warnings when it should (@test-contrasts.R#15) 
  3. Failure: clm gives contrast warnings when it should (@test-contrasts.R#19) 
  4. Failure: clm gives contrast warnings when it should (@test-contrasts.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [33s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(origami)
  origami: Generalized Cross-Validation Framework
  Version: 1.0.0
  > library(data.table)
  > test_check("origami")
  ── 1. Failure: CV MSE matches previous value (@test-overall.R#36)  ─────────────
  `cv_MSE` not equal to 13.32.
  1/1 mismatches
  [1] 14.1 - 13.3 == 0.791
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 34 SKIPPED: 0 FAILED: 1
  1. Failure: CV MSE matches previous value (@test-overall.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  ../osqp_sources//include/glob_opts.h:173:50: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic]
See ‘/data/gannet/ripley/R/packages/tests-devel/osqp.Rcheck/00install.out’ for details.
Running ‘testthat_chi2.R’ [6s/21s]
  Running ‘testthat_extractSubTree.R’ [24s/81s]
  Running ‘testthat_pacotestRegressionTests.R’ [8s/25s]
  Running ‘testthat_pacotestRvineSeqRegressionTests.R’ [62s/227s]
  Running ‘testthat_pacotestRvineSingleCopulaRegressionTests.R’ [3m/12m]
Running the tests in ‘tests/testthat_pacotestRvineSeqRegressionTests.R’ failed.
Complete output:
  > 
  > library("testthat")
  > library("pacotest")
  > 
  > test_check("pacotest", filter = "pacotestRvineSeqRegressionTests")
  ── 1. Failure: pacotestRvineSeq7 (@test-pacotestRvineSeqRegressionTests.R#194)  
  resPacotestComputed[iTest, 1:3] not equal to hardCodedResPacotestRvineSeq[iTest, 1:3].
  1/3 mismatches
  [2] 0.768 - 0.755 == 0.013
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 4 SKIPPED: 5 FAILED: 1
  1. Failure: pacotestRvineSeq7 (@test-pacotestRvineSeqRegressionTests.R#194) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(padr)
  > 
  > test_check("padr")
  ── 1. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#
  fill_by_function(x_df, y1)$y1 %>% median not equal to 14.77.
  1/1 mismatches
  [1] 14.8 - 14.8 == 0.04
  
  ── 2. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#
  fill_by_function(x_df, y1, y2)$y1 %>% median not equal to 14.77.
  1/1 mismatches
  [1] 14.8 - 14.8 == 0.04
  
  ── 3. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#
  fill_by_function(x_df, y1, y2)$y2 %>% median not equal to 22.765.
  1/1 mismatches
  [1] 25.3 - 22.8 == 2.5
  
  ── 4. Failure: fill_by_prevalent gives expected outcomes (@test_fill_functions.R
  `fill_by_prevalent(x_df, y1)` did not throw an error.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 584 SKIPPED: 1 FAILED: 4
  1. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#36) 
  2. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#37) 
  3. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#38) 
  4. Failure: fill_by_prevalent gives expected outcomes (@test_fill_functions.R#48) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [11s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(palasso)
  > 
  > testthat::test_check("palasso")
  ── 1. Failure: deviance stats (@test.R#146)  ───────────────────────────────────
  `x` isn't true.
  
  ── 2. Error: coef stats (@test.R#126)  ─────────────────────────────────────────
  attempt to select less than one element in get1index
  1: coef(fit, model = "standard_xz", s = 0) at testthat/test.R:126
  2: coef.palasso(fit, model = "standard_xz", s = 0)
  3: subset.palasso(x = object, model = model, max = max)
  
  ── 3. Error: deviance stats (@test.R#142)  ─────────────────────────────────────
  attempt to select less than one element in get1index
  1: deviance(fit, model = "standard_xz") at testthat/test.R:142
  2: deviance.palasso(fit, model = "standard_xz")
  3: subset.palasso(x = object, model = model, max = max)
  
  ── 4. Error: logLik stats (@test.R#150)  ───────────────────────────────────────
  attempt to select less than one element in get1index
  1: logLik(fit, model = "standard_xz") at testthat/test.R:150
  2: logLik.palasso(fit, model = "standard_xz")
  3: subset.palasso(x = object, model = model, max = max)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2107 SKIPPED: 2 FAILED: 4
  1. Failure: deviance stats (@test.R#146) 
  2. Error: coef stats (@test.R#126) 
  3. Error: deviance stats (@test.R#142) 
  4. Error: logLik stats (@test.R#150) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  fdouble_metaphone.c:268:5: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/PGRdup.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [12s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > suppressPackageStartupMessages(library(phangorn))
  > 
  > test_check("phangorn")
  loglik: -11409.87 --> -11409.87 
  ── 1. Failure: SPR distance (@test_treedist.R#100)  ────────────────────────────
  SPR.dist(tree1, trees) not equal to 1:5.
  1/5 mismatches
  [2] 1 - 2 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 120 SKIPPED: 28 FAILED: 1
  1. Failure: SPR distance (@test_treedist.R#100) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘test-all.R’ [14s/14s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > options(poppr.debug = TRUE)
  > test_check("poppr")
  Loading required package: poppr
  Loading required package: adegenet
  Loading required package: ade4
  
     /// adegenet 2.1.1 is loaded ////////////
  
     > overview: '?adegenet'
     > tutorials/doc/questions: 'adegenetWeb()' 
     > bug reports/feature requests: adegenetIssues()
  
  
  This is poppr version 2.8.1. To get started, type package?poppr
  OMP parallel support: available
  ── 1. Failure: rrmlg produces the correct mlgs (@test-round-robin.R#24)  ───────
  `rrx_m` not equivalent to `mlg_truth`.
  11/15 mismatches (average diff: 1.73)
  [2]  3 - 2 ==  1
  [3]  2 - 3 == -1
  [5]  4 - 1 ==  3
  [6]  1 - 2 == -1
  [7]  3 - 4 == -1
  [9]  1 - 3 == -2
  [10] 4 - 1 ==  3
  [12] 4 - 3 ==  1
  [13] 3 - 2 ==  1
  ...
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 308 SKIPPED: 186 FAILED: 1
  1. Failure: rrmlg produces the correct mlgs (@test-round-robin.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘intro_pfit.Rmd’ using rmarkdown
PP package calling ...
Follow this project on github: https://github.com/manuelreif/PP.git
Quitting from lines 131-155 (intro_pfit.Rmd) 
Error: processing vignette 'intro_pfit.Rmd' failed with diagnostics:
'x' contains missing values
--- failed re-building ‘intro_pfit.Rmd’

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

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

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  zhegv.c:216:27: warning: ‘strncpy’ specified bound 2 equals destination size [-Wstringop-truncation]
  zhegv.c:216:27: warning: ‘strncpy’ specified bound 3 equals destination size [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/PRIMME.Rcheck/00install.out’ for details.
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.
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.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(qwraps2)
  > 
  > test_check("qwraps2")
  ── 1. Failure: Boot Strap (@test-confusion_matrix.R#15)  ───────────────────────
  round(con_mat_boot$stats[, "Boot Est"], 3) not equivalent to c(0.573, 0.669, 0.532, 0.382, 0.788).
  5/5 mismatches (average diff: 0.003)
  [1] 0.570 - 0.573 == -0.003
  [2] 0.670 - 0.669 ==  0.001
  [3] 0.527 - 0.532 == -0.005
  [4] 0.377 - 0.382 == -0.005
  [5] 0.789 - 0.788 ==  0.001
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 49 SKIPPED: 0 FAILED: 1
  1. Failure: Boot Strap (@test-confusion_matrix.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  R4dfp-object.c:253:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
  R4dfp-object.c:260:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/R4dfp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/race.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [14s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rags2ridges)
  > 
  > test_check("rags2ridges")
  ── 1. Failure: armaRidgeP.fused agrees with the old R implmentation (@test-armaR
  isTRUE(...) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 3893 SKIPPED: 0 FAILED: 1
  1. Failure: armaRidgeP.fused agrees with the old R implmentation (@test-armaRidgeP.fused.R#149) 
  
  Error: testthat unit tests failed
  Execution halted
.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 significant warnings:
  avc_binwr.c:166:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:173:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:180:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:187:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:1453:29: warning: ‘%4.4d’ directive writing between 4 and 10 bytes into a region of size 5 [-Wformat-overflow=]
  avc_binwr.c:1553:28: warning: ‘%s’ directive writing up to 39 bytes into a region of size between 38 and 77 [-Wformat-overflow=]
  avc_e00write.c:386:30: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  avc_e00write.c:387:30: warning: ‘-ID’ directive writing 3 bytes into a region of size between 1 and 40 [-Wformat-overflow=]
  avc_e00write.c:401:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:397:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:409:39: warning: ‘%s’ directive writing up to 39 bytes into a region of size 33 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/RArcInfo.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rreadsdpa.c:608:15: warning: ‘strncpy’ output may be truncated copying 3999 bytes from a string of length 3999 [-Wstringop-truncation]
  Rreadsdpa.c:1041:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  Rreadsdpa.c:1042:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:164:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:165:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/Rdsdp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  compile.cc:292:69: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class re2::Prog::Inst’; use assignment or value-initialization instead [-Wclass-memaccess]
  regexp.cc:343:33: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
  regexp.cc:344:32: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
See ‘/data/gannet/ripley/R/packages/tests-devel/re2r.Rcheck/00install.out’ for details.
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 significant warnings:
  phonet.c:1207:34: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  phonet.c:1208:34: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/RecordLinkage.Rcheck/00install.out’ for details.
Found the following significant warnings:
  cornellout.cpp:99:20: warning: ‘%2d’ directive writing between 2 and 11 bytes into a region of size between 0 and 931 [-Wformat-overflow=]
  cornellout.cpp:137:26: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  cornellout.cpp:129:26: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 988 and 995 [-Wformat-overflow=]
  mat.cpp:315:4: warning: ‘*<unknown>.dataMat::p’ is used uninitialized in this function [-Wuninitialized]
  tilia.cpp:179:14: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 61 bytes from a string of length 199 [-Wstringop-truncation]
  tilia.cpp:180:10: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 19 bytes from a string of length 19 [-Wstringop-truncation]
  tilia.cpp:225:14: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 8 bytes from a string of length 199 [-Wstringop-truncation]
  tilia.cpp:228:17: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 8 bytes from a string of length 29 [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/rioja.Rcheck/00install.out’ for details.
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:
  RngStream.c:347:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/rlecuyer.Rcheck/00install.out’ for details.
Found the following significant warnings:
  origcmaes.cc:2852:13: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  origcmaes.cc:2855:12: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  origcmaes.cc:2858:12: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/Rmalschains.Rcheck/00install.out’ for details.
Found the following significant warnings:
  DbResult.cpp:81:41: warning: catching polymorphic type ‘class MariaResultPrep::UnsupportedPS’ by value [-Wcatch-value=]
See ‘/data/gannet/ripley/R/packages/tests-devel/RMariaDB.Rcheck/00install.out’ for details.
Running examples in ‘rms-Ex.R’ failed
The error most likely occurred in:

> ### Name: Function
> ### Title: Compose an S Function to Compute X beta from a Fit
> ### Aliases: Function.rms Function.cph sascode perlcode
> ### Keywords: regression methods interface models survival math
> 
> ### ** Examples
> 
> set.seed(1331)
> x1 <- exp(rnorm(100))
> x2 <- factor(sample(c('a','b'),100,rep=TRUE))
> dd <- datadist(x1, x2)
> options(datadist='dd')
> y  <- log(x1)^2+log(x1)*(x2=='b')+rnorm(100)/4
> f  <- ols(y ~ pol(log(x1),2)*x2)
> f$coef
   Intercept           x1         x1^2         x2=b    x1 * x2=b  x1^2 * x2=b 
-0.001885864 -0.019198566  1.017432226  0.047810769  1.037259829 -0.032005994 
> g  <- Function(f, digits=5)
> g
function (x1 = 1.0906, x2 = "b") 
{
    x1 <- log(x1)
    -0.0018859 - 0.019199 * x1 + 1.0174 * x1^2 + 0.047811 * (x2 == 
        "b") + (x2 == "b") * (1.0373 * x1 - 0.032006 * x1^2)
}
<environment: 0x97fa4e8>
> sascode(g)
    x1 = log(x1)
    -0.0018859 - 0.019199 * x1 + 1.0174 * x1**2 + 0.047811 * (x2 = 
        "b") + (x2 = "b") * (1.0373 * x1 - 0.032006 * x1**2);
> cat(perlcode(g), '\n')
Error in expr[[3]] : subscript out of bounds
Calls: cat ... convert -> f -> paste -> convert -> f -> paste -> convert
Execution halted
Found the following significant warnings:
  nxsreader.cpp:659:22: warning: catching polymorphic type ‘class NxsException’ by value [-Wcatch-value=]
  nxsreader.cpp:709:25: warning: catching polymorphic type ‘class NxsException’ by value [-Wcatch-value=]
See ‘/data/gannet/ripley/R/packages/tests-devel/rncl.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [10s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rnn)
  > 
  > test_check("rnn")
  ── 1. Failure: (unknown) (@test_rnn.R#66)  ─────────────────────────────────────
  sum(bin2int(B)) not equal to 888626.
  1/1 mismatches
  [1] 374720 - 888626 == -513906
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test_rnn.R#66) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  robust.cpp:665:25: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=]
See ‘/data/gannet/ripley/R/packages/tests-devel/robfilter.Rcheck/00install.out’ for details.
Found the following significant warnings:
  bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
  rph_tfbs.c:371:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:351:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:819:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/rphast.Rcheck/00install.out’ for details.
Output from running autoconf:
  configure.ac:92: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
  ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
  ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from...
  ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from...
  ../../lib/autoconf/c.m4:1444: AC_C_BIGENDIAN is expanded from...
  configure.ac:92: the top level
  configure.ac:166: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
  ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
  ../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from...
  ../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from...
  configure.ac:166: the top level
  configure.ac:58: error: possibly undefined macro: AM_CONDITIONAL
        If this token and others are legitimate, please use m4_pattern_allow.
        See the Autoconf documentation.
Non-standard files/directories found at top level:
  ‘clients’ ‘clients.txt’ ‘version’
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.
Running ‘testthat.R’ [57s/63s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("RSSL")
  Loading required package: RSSL
  ── 1. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#53)
  sum(predict(g_sup, problem$X_test) == problem$y_test) not equal to 61.
  1/1 mismatches
  [1] 55 - 61 == -6
  
  ── 2. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#54)
  sum(predict(g_semi, problem$X_test) == problem$y_test) not equal to 61.
  1/1 mismatches
  [1] 55 - 61 == -6
  
  ── 3. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#55)
  sum(predict(g_euc, problem$X_test) == problem$y_test) not equal to 57.
  1/1 mismatches
  [1] 55 - 57 == -2
  
  ── 4. Failure: Multiclass gives an output (@test-LeastSquaresClassifier.R#46)  ─
  sum(...) not equal to 61.
  1/1 mismatches
  [1] 60 - 61 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 466 SKIPPED: 0 FAILED: 4
  1. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#53) 
  2. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#54) 
  3. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#55) 
  4. Failure: Multiclass gives an output (@test-LeastSquaresClassifier.R#46) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  RngStreams.c:332:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/rstream.Rcheck/00install.out’ for details.
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 significant warnings:
  bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
  rph_tfbs.c:371:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:351:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:819:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/rtfbs.Rcheck/00install.out’ for details.
Found the following significant warnings:
  geometry/s2loop.cc:85:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2loop.cc:247:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2polyline.cc:52:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2polyline.cc:94:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2regioncoverer.cc:119:28: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct S2RegionCoverer::Candidate’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess]
See ‘/data/gannet/ripley/R/packages/tests-devel/s2.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.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/scio.Rcheck/00install.out’ for details.
Found the following significant warnings:
  catnet_rexport.cpp:221:17: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:229:15: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:237:16: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
  catnet_rexport.cpp:240:18: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:241:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:258:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:257:18: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/sdnet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/sdwd.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [17s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("sentimentr")
  > 
  > test_check("sentimentr")
  ── 1. Failure: extract_sentiment_terms extracts the terms (@test-extract_sentime
  pol_words$negative[1:3] not equal to list(character(0), c("wait", "restless", "fire"), character(0)).
  Component 2: Lengths (0, 3) differ (string compare on first 0)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 32 SKIPPED: 0 FAILED: 1
  1. Failure: extract_sentiment_terms extracts the terms (@test-extract_sentiment_terms.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sigmajs)
  Welcome to sigmajs
  
  Docs: sigmajs.john-coene.com
  > 
  > test_check("sigmajs")
  Found # 3 clusters
  ── 1. Failure: delay (@test-graph.R#50)  ───────────────────────────────────────
  unlist(unname(sg$x$addNodesDelay[[1]][5])) not equal to " 566.004".
  1/1 mismatches
  x[1]: " 548.9736"
  y[1]: " 566.004"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 65 SKIPPED: 0 FAILED: 1
  1. Failure: delay (@test-graph.R#50) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [14s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(slouch)
  > 
  > # testsetup <- function(){
  > #   pars <- list(myfunc = myfunc, dummydata = dummydata, model.id.btk = model.id.btk)
  > #   return(pars)
  > # }
  > 
  > test_check("slouch")
  ── 1. Failure: No errors ANOVA (@test_anova.R#37)  ─────────────────────────────
  structure(...) not equal to m1$beta_primary$coefficients.
  3/4 mismatches (average diff: 0.0444)
  [1] 0.4216 - 0.4893 == -0.06774
  [2] 0.4815 - 0.4220 ==  0.05951
  [4] 0.0504 - 0.0445 ==  0.00591
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 9 SKIPPED: 0 FAILED: 1
  1. Failure: No errors ANOVA (@test_anova.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [4s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # setting R_TESTS to empty string because of
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # revert this when that issue in R is fixed.
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(Smisc)
  > 
  > # There shouldn't be any files in the tmp folder
  > unlink("testthat/tmp", recursive = TRUE, force = TRUE)
  > dir.create("testthat/tmp")
  > 
  > test_check("Smisc")
  ── 1. Failure: parseJob() doesn't deviate from historical behavior (@test_parseJ
  `xout` not equal to `xin`.
  Component "x2": Component 1: Mean relative difference: 0.8461538
  Component "x2": Component 2: Mean relative difference: 0.7532468
  Component "x2": Component 3: Mean relative difference: 0.5416667
  Component "x2": Component 4: Mean relative difference: 0.34375
  Component "x2": Component 5: Mean relative difference: 0.5441176
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 275 SKIPPED: 0 FAILED: 1
  1. Failure: parseJob() doesn't deviate from historical behavior (@test_parseJob.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘test-all.R’ [95s/329s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.tools")
  Loading required package: SpaDES.tools
  ── 1. Failure: spread produces legal RasterLayer (@test-spread.R#60)  ──────────
  all(...) isn't true.
  
  ── 2. Failure: spreadProb with relative values does not work correctly (@test-sp
  sum(hab3[events1[] > 0]) > sum(hab3[events2[] > 0]) isn't true.
  
  ── 3. Failure: spread2 tests (@test-spread2.R#220)  ────────────────────────────
  cht$p.value > 0.05 isn't true.
  
  [1] "Scales with number of starts, not maxSize of raster"
  ── 4. Failure: spread2 tests -- asymmetry (@test-spread2.R#710)  ───────────────
  circs[sams] == circs[ciCentre[] == 1] isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1048 SKIPPED: 11 FAILED: 4
  1. Failure: spread produces legal RasterLayer (@test-spread.R#60) 
  2. Failure: spreadProb with relative values does not work correctly (@test-spread.R#1259) 
  3. Failure: spread2 tests (@test-spread2.R#220) 
  4. Failure: spread2 tests -- asymmetry (@test-spread2.R#710) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [31s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(spew)
  > 
  > test_check("spew")
  ── 1. Error: Moment Matching (@test-sampling.R#32)  ────────────────────────────
  abs(2.8 - mean(pums[inds, ]$NP)) < 0.05 is not TRUE
  1: stopifnot(abs(2.8 - mean(pums[inds, ]$NP)) < 0.05) at testthat/test-sampling.R:32
  
  [1] "Place has 0 Households!"
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 101 SKIPPED: 7 FAILED: 1
  1. Error: Moment Matching (@test-sampling.R#32) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(splitstackshape)
  > 
  > test_check("splitstackshape")
  ── 1. Failure: stratified returns the expected number of rows (@test_stratified.
  nrow(stratified(DF, "A", 0.1, select = list(A = c("AA", "BB")))) not equal to 3.
  1/1 mismatches
  [1] 4 - 3 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 51 SKIPPED: 0 FAILED: 1
  1. Failure: stratified returns the expected number of rows (@test_stratified.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  dbfopenSSN.c:1119:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:1100:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:663:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopenSSN.c:1511:2: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/SSN.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘HTML_special_features.Rmd’ using rmarkdown
--- finished re-building ‘HTML_special_features.Rmd’

--- re-building ‘Rmarkdown.Rmd’ using rmarkdown
pandoc: Cannot decode byte '\xa9': Data.Text.Internal.Encoding.streamDecodeUtf8With: Invalid UTF-8 stream
Error: processing vignette 'Rmarkdown.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
--- failed re-building ‘Rmarkdown.Rmd’

--- re-building ‘code_chunks.Rmd’ using rmarkdown
pandoc: Cannot decode byte '\xa9': Data.Text.Internal.Encoding.streamDecodeUtf8With: Invalid UTF-8 stream
Error: processing vignette 'code_chunks.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
--- failed re-building ‘code_chunks.Rmd’

--- re-building ‘stationery.Rnw’ using Sweave
--- finished re-building ‘stationery.Rnw’

SUMMARY: processing the following files failed:
  ‘Rmarkdown.Rmd’ ‘code_chunks.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  computeQ.cpp:75:15: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
  computeQ.cpp:134:15: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
  computeQ.cpp:142:17: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
See ‘/data/gannet/ripley/R/packages/tests-devel/strum.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [20s/37s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("STV")
  Loading required package: STV
  ── 1. Failure: Toy example (@testExt.R#36)  ────────────────────────────────────
  `x` not equal to `expected`.
  1/4 mismatches
  x[2]: "ATL_54"
  y[2]: "ATL_27"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 4 SKIPPED: 0 FAILED: 1
  1. Failure: Toy example (@testExt.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  rapi.cc:191:12: warning: catching polymorphic type ‘struct subprocess::subprocess_exception’ by value [-Wcatch-value=]
See ‘/data/gannet/ripley/R/packages/tests-devel/subprocess.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Different type kinds at (1)
  Warning: GNU Extension: initialization of common block variable ‘iset’ in DATA statement at (1)
  Warning: GNU Extension: Variable ‘iset’ at (1) is in COMMON but only in BLOCK DATA initialization is allowed
  Warning: GNU Extension: Missing comma at (1)
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1) [-Wcharacter-truncation]
  Warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘cnop’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1) [-Wcharacter-truncation]
  Warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/SWATmodel.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [162s/180s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(TauStar)
  > 
  > test_check("TauStar")
  ── 1. Failure: tauStarTest with mixed data. (@test_tauStarTest.R#89)  ──────────
  abs(a$pVal - (1 - pMixHoeffInd(n * tval, p))) <= 10^-2 isn't true.
  
  ── 2. Failure: tauStarTest with mixed data. (@test_tauStarTest.R#89)  ──────────
  abs(a$pVal - (1 - pMixHoeffInd(n * tval, p))) <= 10^-2 isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 529 SKIPPED: 0 FAILED: 2
  1. Failure: tauStarTest with mixed data. (@test_tauStarTest.R#89) 
  2. Failure: tauStarTest with mixed data. (@test_tauStarTest.R#89) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  /data/gannet/ripley/R/test-3.6/sparsepp/include/sparsepp/spp_utils.h:422:44: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair<const std::pair<unsigned int, unsigned int>, int>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess]
  /data/gannet/ripley/R/test-3.6/sparsepp/include/sparsepp/spp_utils.h:422:44: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair<const std::pair<unsigned int, unsigned int>, float>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess]
See ‘/data/gannet/ripley/R/packages/tests-devel/text2vec.Rcheck/00install.out’ for details.
Found the following significant warnings:
  RngStream.c:347:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/TPmsm.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.
Found the following significant warnings:
  libqhull/rboxlib.c:351:5: warning: ‘strncat’ output may be truncated copying between 0 and 199 bytes from a string of length 199 [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/TukeyRegion.Rcheck/00install.out’ for details.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/uavRst.Rcheck/00install.out’ for details.
Running ‘test_unifDAG.R’
Running the tests in ‘tests/test_unifDAG.R’ failed.
Complete output:
  > library(unifDAG)
  > 
  > my.wgtMatrix <- function(g, transpose = TRUE) {
  +   res <- as(g, "matrix") # from 'graph' package, now reliable (we hope)
  +   if (transpose) ## default!
  +     t(res) else res
  + }
  > 
  > ## exact
  > set.seed(123)
  > n <- 2
  > reps <- 100
  > res <- matrix(0, reps, 3)
  > for (i in 1:reps) {
  +     gAM <- unifDAG(n)
  +     wm <- my.wgtMatrix(gAM)
  +     if (wm[1,2] != 0) {
  +         res[i,1] <- 1
  +     } else {
  +           if (wm[2,1] != 0) {
  +               res[i,2] <- 1
  +           } else {
  +                 res[i,3] <- 1
  +             }
  +       }
  + }
  > if (!all(round(colMeans(res), 2) == c(0.41, 0.31, 0.28))) {
  +     stop("test_unifDAG: Saved result could not be reproduced (unifDAG).")
  + }
  Error: test_unifDAG: Saved result could not be reproduced (unifDAG).
  Execution halted
Running ‘testthat.R’ [25s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(utiml)
  Loading required package: mldr
  Loading required package: parallel
  > 
  > test_check("utiml")
  ── 1. Failure: Bipartition measures (@test_evaluation.R#153)  ──────────────────
  mean(utiml_measure_macro_f1(mlconfmat)) not equal to measures$MacroFMeasure.
  1/1 mismatches
  [1] 0.275 - NaN == NaN
  
  ── 2. Failure: iterative kfold (@test_sampling.R#238)  ─────────────────────────
  length(f1$fold[[2]]) not equal to 25.
  1/1 mismatches
  [1] 24 - 25 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1155 SKIPPED: 21 FAILED: 2
  1. Failure: Bipartition measures (@test_evaluation.R#153) 
  2. Failure: iterative kfold (@test_sampling.R#238) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<> >::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::MemoryPoolAllocator<> >’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<> >’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::CrtAllocator>’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/data/gannet/ripley/R/packages/tests-devel/validatejsonr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  tabix/razf.c:188:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/WhopGenome.Rcheck/00install.out’ for details.
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’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(WMWssp)
  > 
  > test_check("WMWssp")
  Simulation:
  
  Wilcoxon-Mann-Whitney Sample Size Calculation
   
  Summary
  Call: eval
  Type-I error (two-sided): 0.05
  Power: 0.8
  
                                   Results
  alpha (2-sided)                0.0500000
  Power                          0.8000000
  Simulated Power                0.7600000
  N (total sample size needed)   0.3491124
  t=n1/N                       111.3664650
  n1 in Group 1                  0.4964905
  n2 in Group 2                 55.2923889
  N rounded for t = 1/2         56.0740762
  N rounded                    112.0000000
  n1 rounded                   113.0000000
  n2 rounded                    56.0000000
  12                            57.0000000
  ── 1. Failure: function WMWssp_minimize (@test_MinMax.R#22)  ───────────────────
  `result_power` not equivalent to `result_simpower`.
  1/1 mismatches
  [1] 0.92 - 0.76 == 0.16
  
  Simulation:
  
  ── 2. Failure: function WMWssp (@test_WMWssp.R#21)  ────────────────────────────
  `result_power` not equivalent to `result_simpower`.
  1/1 mismatches
  [1] 0.9 - 0.7 == 0.2
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 14 SKIPPED: 0 FAILED: 2
  1. Failure: function WMWssp_minimize (@test_MinMax.R#22) 
  2. Failure: function WMWssp (@test_WMWssp.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [62s/63s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(xgboost)
  > 
  > test_check("xgboost")
  [1]	train-error:0.061262 
  ── 1. Failure: xgb.cv works (@test_basic.R#185)  ───────────────────────────────
  cv$evaluation_log[, min(test_error_std)] is not strictly less than 0.004. Difference: 0.00328
  
  [1]	train-logloss:0.380601 
  [2]	train-logloss:0.247327 
  [3]	train-logloss:0.175046 
  [4]	train-logloss:0.122303 
  [5]	train-logloss:0.089890 
  [1]	train-logloss:0.497351 
  [2]	train-logloss:0.357289 
  [3]	train-logloss:0.257217 
  [4]	train-logloss:0.184524 
  [5]	train-logloss:0.132112 
  [1]	train-auc:0.900000	test-auc:0.800000 
  ── 2. Failure: prediction in early-stopping xgb.cv works (@test_callbacks.R#301)
  abs(err_pred - err_log_last) is not strictly more than 1e-04. Difference: -9.99e-05
  
  [1]	eval-error:0.042831	train-error:0.046522 
  [2]	eval-error:0.021726	train-error:0.022263 
  [1]	eval-error:0.042831	train-error:0.046522 
  [2]	eval-error:0.021726	train-error:0.022263 
  [1]	train-error:0.046522 
  [2]	train-error:0.022263 
  [1]	train-error:0.333333 
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 562 SKIPPED: 4 FAILED: 2
  1. Failure: xgb.cv works (@test_basic.R#185) 
  2. Failure: prediction in early-stopping xgb.cv works (@test_callbacks.R#301) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/zonator.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    bootstrapping_example   1.1Mb
    libs                    3.5Mb
Running examples in 'adamethods-Ex.R' failed
The error most likely occurred in:

> ### Name: do_alphas_rss
> ### Title: Alphas and RSS of every set of archetypoids
> ### Aliases: do_alphas_rss
> 
> ### ** Examples
> 
> data(mtcars)
> data <- mtcars
> n <- nrow(data)
> m <- 10
> 
> k <- 3 
> numRep <- 2
> huge <- 200
> 
> set.seed(1)
> rand_obs_si <- sample(1:n, size = m) 
> 
> si <- data[rand_obs_si,]
> ada_si <- do_ada(si, k, numRep, huge, FALSE) 
Warning in archetypes_norm_frob(data, k = numArch[i], saveHistory = FALSE,  :
  k=3: Error in qr.solve(alphas %*% t(alphas)): singular matrix 'a' in solve

Warning in archetypes_norm_frob(data, k = numArch[i], saveHistory = FALSE,  :
  k=3: Error in qr.solve(alphas %*% t(alphas)): singular matrix 'a' in solve

Error in archetypoids_norm_frob(numArchoid, subset, huge = huge, ArchObj = lass) : 
  No archetypes computed
Calls: do_ada -> archetypoids_norm_frob
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.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.7Mb
    pictures   2.1Mb
Running examples in 'adehabitatMA-Ex.R' failed
The error most likely occurred in:

> ### Name: buffer
> ### Title: Compute Buffers Regions
> ### Aliases: buffer
> ### Keywords: spatial
> 
> ### ** Examples
> 
> 
> data(lynxjura)
> 
> # locs is the SpatialPointsDataFrame containing the
> # locations of lynx indices in the Jura mountains
> locs <- lynxjura$locs
> head(locs)
        coordinates     Date Type
3 (856208, 2135450) 19801231   EP
4 (852942, 2134370) 19810101   EP
5 (857408, 2134780) 19810101    E
7 (857425, 2135190) 19810114    E
8 (853543, 2133730) 19810114    E
9 (852771, 2132560) 19810114    E
Coordinate Reference System (CRS) arguments: NA 
> 
> ## just for the sake of illustration: sample 100 points
> set.seed(233)
> locs <- locs[sample(1:nrow(locs), 100),]
> 
> # sa is the SpatialPixelsDataFrame object containing
> # maps of the study area
> sa <- lynxjura$map
> 
> # Buffer of 2000 m from all points
> bu <- buffer(locs, sa, 2000)
> image(bu)
> 
> # displays all the pixels of the study area within 2000 m
> # of a point, for each type of indices (see ?lynxjura)
> buani <- buffer(locs[,2], sa, 2000)
> buani
Object of class "SpatialPixelsDataFrame" (package sp):

Grid parameters:
  cellcentre.offset cellsize cells.dim
x            828916      500        96
y           2130700      500        90

Variables measured:
  D E EF EO EP L O OP P
1 0 0  0  0  0 0 0  0 0
2 0 0  0  0  0 0 0  0 0
3 0 0  0  0  0 0 0  0 0
4 0 0  0  0  0 0 0  0 0
5 0 0  0  0  0 0 0  0 0
6 0 0  0  0  0 0 0  0 0
...

> par(mar=c(0,0,2,0))
> opar<-par(mfrow=c(3,4))
> lapply(1:11, function(i) {
+    image(buani, i)
+    title(main = names(slot(buani, "data"))[i])
+ })
Error in `[.data.frame`(x@data, , i, drop = FALSE) : 
  undefined columns selected
Calls: lapply ... matrix -> t -> matrix -> [ -> [ -> [ -> [.data.frame
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/AeRobiology.Rcheck/00install.out' for details.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    data  15.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
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  5.3Mb
  sub-directories of 1Mb or more:
    help   4.7Mb
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(anonymizer)
  > 
  > test_check("anonymizer")
  -- 1. Failure: Produces the correct output. (@test-anonymize.R#5)  -------------
  anonymize("a", .seed = 1) not equal to "ed879445e47969394b3f8eb818501976bed22b9ab0e7f7c5fdf2a96df0aec80e".
  1/1 mismatches
  x[1]: "6ae80dd07643618a5ea6ac83b506fd367d81f86e5f5650a42045ca7ebe516602"
  y[1]: "ed879445e47969394b3f8eb818501976bed22b9ab0e7f7c5fdf2a96df0aec80e"
  
  -- 2. Failure: Produces the correct output. (@test-salt.R#6)  ------------------
  salt("a", .seed = 1, .n_chars = 1) not equal to "gag".
  1/1 mismatches
  x[1]: "yay"
  y[1]: "gag"
  
  -- 3. Failure: Produces the correct output. (@test-salt.R#7)  ------------------
  salt("a", .seed = 2, .n_chars = 1) not equal to "eae".
  1/1 mismatches
  x[1]: "uau"
  y[1]: "eae"
  
  == testthat results  ===========================================================
  OK: 12 SKIPPED: 1 FAILED: 3
  1. Failure: Produces the correct output. (@test-anonymize.R#5) 
  2. Failure: Produces the correct output. (@test-salt.R#6) 
  3. Failure: Produces the correct output. (@test-salt.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
Running examples in 'Anthropometry-Ex.R' failed
The error most likely occurred in:

> ### Name: projShapes
> ### Title: Helper function for plotting the shapes
> ### Aliases: projShapes
> ### Keywords: math
> 
> ### ** Examples
> 
> landmarksNoNa <- na.exclude(landmarksSampleSpaSurv)
> dim(landmarksNoNa) 
[1] 574 198
> #[1] 574 198 
> numLandmarks <- (dim(landmarksNoNa)[2]) / 3
> #[1] 66
> #As a toy example, only the first 15 individuals are used.
> landmarksNoNa_First10 <- landmarksNoNa[1:10, ] 
> (numIndiv <- dim(landmarksNoNa_First10)[1])
[1] 10
> #[1] 10         
>     
> array3D <- array3Dlandm(numLandmarks, numIndiv, landmarksNoNa_First10)
> #shapes::plotshapes(array3D[,,1]) 
> #calibrate::textxy(array3D[,1,1], array3D[,2,1], labs = 1:numLandmarks, cex = 0.7) 
> 
> numClust <- 2 ; algSteps <- 1 ; niter <- 1 ; stopCr <- 0.0001
> resLL <- LloydShapes(array3D, numClust, algSteps, niter, stopCr, FALSE, FALSE)
> clust_kmeansProc <- resLL$asig
> 
> prototypes <- anthrCases(resLL)
> 
> projShapes(1, array3D, clust_kmeansProc, prototypes)
Error in if (d2 == 0L) { : missing value where TRUE/FALSE needed
Calls: projShapes -> <Anonymous> -> procrustesGPA -> cnt3 -> apply
Execution halted
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/winapi/basic_types.hpp:212:44: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/winapi/basic_types.hpp:213:53: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.6/anytime.Rcheck/00install.out' for details.
installed size is 73.0Mb
  sub-directories of 1Mb or more:
    gdal   3.8Mb
    libs  68.8Mb
Running 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(aphid)
  > 
  > test_check("aphid")
  -- 1. Failure: Character and raw inputs give same output (@test_PHMM.R#137)  ---
  round(x.vit$score) not equal to round(xDNA.vit$score).
  1/1 mismatches
  [1] 90 - 91 == -1
  
  == testthat results  ===========================================================
  OK: 45 SKIPPED: 0 FAILED: 1
  1. Failure: Character and raw inputs give same output (@test_PHMM.R#137) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [18s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(aphid)
  > 
  > test_check("aphid")
  -- 1. Failure: Character and raw inputs give same output (@test_PHMM.R#137)  ---
  round(x.vit$score) not equal to round(xDNA.vit$score).
  1/1 mismatches
  [1] 90 - 91 == -1
  
  == testthat results  ===========================================================
  OK: 44 SKIPPED: 0 FAILED: 1
  1. Failure: Character and raw inputs give same output (@test_PHMM.R#137) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'archetypes-Ex.R' failed
The error most likely occurred in:

> ### Name: simplexplot
> ### Title: Simplex visualization
> ### Aliases: simplexplot
> 
> ### ** Examples
> 
> ### This example reproduces parts of the Figure 7 shown in
>   ### "Probabilistic Archetypal Analysis" by Seth and Eugster (2014)
> 
>   data("toy", package = "archetypes")
> 
>   set.seed(1234); a3 <- archetypes(toy, k = 3)
>   set.seed(1237); a4 <- archetypes(toy, k = 4)
>   set.seed(1238); a5 <- archetypes(toy, k = 5)
Warning in archetypes(toy, k = 5) :
  k=5: Error in qr.solve(alphas %*% t(alphas)): singular matrix 'a' in solve

> 
>   simplexplot(a3)
>   simplexplot(a3, show_direction = TRUE, show_points = FALSE)
>   simplexplot(a4, projection = tspsimplex_projection)
Loading required package: TSP
>   simplexplot(a5, show_direction = TRUE, show_points = FALSE,
+     direction_length = 2, directions_col = "black")
Error in rep(points_col, nrow(coef(object))) : invalid 'times' argument
Calls: simplexplot
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   1.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.5Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    bin   12.0Mb
    misc   2.1Mb
Package suggested but not available for checking: 'REBayes'
Running examples in 'assist-Ex.R' failed
The error most likely occurred in:

> ### Name: anova.ssr
> ### Title: Testing a Non-parametric Function Fitted via Smoothing Splines
> ### Aliases: anova.ssr
> ### Keywords: file
> 
> ### ** Examples
> 
> data(acid)
> 
> # fit a partial thin-plate spline
> temp <- ssr(ph~t1+x1+x2, rk=tp(t1), data=acid, spar="m")
At line 1992 of file rkpk1.f
Fortran runtime error: Index '2' of dimension 1 of array 'jpvt' above upper bound of 1
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.6/audio.Rcheck/00install.out' for details.
Package which this enhances but not available for checking: 'rPython'
installed size is 46.8Mb
  sub-directories of 1Mb or more:
    libs  46.1Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    java   7.4Mb
Running examples in 'AWR.Kinesis-Ex.R' failed
The error occurred in:


R Under development (unstable) (2019-03-03 r76192) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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

  Natural language support but running in an English locale

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

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

> pkgname <- "AWR.Kinesis"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> library('AWR.Kinesis')
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
Error: connections left open:
	stdin (file)
Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   1.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    libs  33.4Mb
Found the following significant warnings:
  Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
See 'd:/Rcompile/CRANpkg/local/3.6/bapred.Rcheck/00install.out' for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.6Mb
    libs   1.9Mb
Packages which this enhances but not available for checking:
  'doMC', 'rPython'
Package suggested but not available for checking: 'doMC'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/BayClone2.Rcheck/00install.out' for details.
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("bayesCT")
  Loading required package: bayesCT
  
  Attaching package: 'bayesCT'
  
  The following object is masked from 'package:stats':
  
      simulate
  
  -- 1. Failure: The randomization is (@test_randomization.R#8)  -----------------
  sum(randomization(12, 10, c(3, 2)) == 1) not equal to 5.
  1/1 mismatches
  [1] 4 - 5 == -1
  
  == testthat results  ===========================================================
  OK: 41 SKIPPED: 0 FAILED: 1
  1. Failure: The randomization is (@test_randomization.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs   2.1Mb
NeedsCompilation field should likely be 'yes'
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   4.1Mb
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
File 'BayHap/libs/i386/BayHap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'mcmc.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'mcmc.o'
File 'BayHap/libs/x64/BayHap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'mcmc.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'mcmc.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Packages suggested but not available for checking: 'bcmapsdata', 'doMC'
Error(s) in re-building vignettes:
--- re-building 'bdlp.Rmd' using rmarkdown
Loading required namespace: RSQLite
Warning: call dbDisconnect() when finished working with a connection
Quitting from lines 197-211 (bdlp.Rmd) 
Error: processing vignette 'bdlp.Rmd' failed with diagnostics:
miller2012.R:7:208: unexpected '{'
6:  
7: miller2012 <- function(setnr = NULL, seedinfo = list(100, "3.6.0", c("Mersenne-Twister", "Inversion", "Rejection", metaseedinfo = list(100, "3.6.0", c("Mersenne-Twister", "Inversion", "Rejecti
                                                                                                                                                                                                                  ^
--- failed re-building 'bdlp.Rmd'

Warning in file.remove(f) :
  cannot remove file 'dangl2014_set_1_seed_100.db', reason 'Permission denied'
SUMMARY: processing the following file failed:
  'bdlp.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
Error(s) in re-building vignettes:
--- re-building 'benthos.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

Quitting from lines 513-514 (benthos.Rmd) 
Error: processing vignette 'benthos.Rmd' failed with diagnostics:
'n' (=100) should be less than the total abundance (=48)
--- failed re-building 'benthos.Rmd'

SUMMARY: processing the following file failed:
  'benthos.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 150.9Mb
  sub-directories of 1Mb or more:
    include  149.9Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/winapi/basic_types.hpp:212:44: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/winapi/basic_types.hpp:213:53: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.6/bigalgebra.Rcheck/00install.out' for details.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/winapi/basic_types.hpp:212:44: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/winapi/basic_types.hpp:213:53: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.6/biganalytics.Rcheck/00install.out' for details.
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
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   2.5Mb
    libs      1.7Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/3.6/bigmemory.Rcheck/00install.out' for details.
Running examples in 'BiG-Ex.R' failed
The error most likely occurred in:

> ### Name: BiG_DA
> ### Title: BiG with half-t prior through a data augmentation approach
> ### Aliases: BiG_DA
> 
> ### ** Examples
> 
> set.seed(1234)
> sim = sim_lvm(G=25, S=6, n_p1=3, rho=runif(6,min=0.3,max=0.9), p_p1=0.6, p_p2=0.8, 
+       lambda=runif(6,min=0.6,max=0.8), n_T=sample(c(5,10,15),6,replace=TRUE))
> BiG_DA(r=sim$r, n_T=sim$n_T, n_p1=3, M=100, burnin=50)
Warning in max(W[which(r[, s] == (n_T[s] + 1)), s]) :
  no non-missing arguments to max; returning -Inf
Error in truncnorm::rtruncnorm(sum(r[, s] == n_T[s] + 1, na.rm = TRUE),  : 
  length(mean) > 0 is not TRUE
Calls: BiG_DA -> <Anonymous> -> stopifnot
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.8Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/winapi/basic_types.hpp:212:44: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/winapi/basic_types.hpp:213:53: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.6/bigtabulate.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   1.9Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Package suggested but not available for checking: 'BiocVersion'
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   8.0Mb
Missing or unexported object: 'gam::step.gam'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.5Mb
Depends: includes the non-default packages:
  'colorspace', 'deldir', 'rgl', 'tcltk', 'tcltk2', 'tkrplot'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'colorspace'
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
install_blat: no visible global function definition for 'download.file'
install_blat: no visible global function definition for 'unzip'
Undefined global functions or variables:
  download.file unzip
Consider adding
  importFrom("utils", "download.file", "unzip")
to your NAMESPACE file.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Running 'testthat.R' [211s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(BMSC)
  Loading required package: Rcpp
  > 
  > test_check("BMSC")
  -- 1. Failure: A message is returned if some rows are missing (@test_missingValu
  `BMSC:::handleMissingData(data, formula, yUncertainty)$data` produced unexpected messages.
  Expected match: 7 rows \\(9.33% of the data\\) were excluded due to missing values.
  Actual values:
  * 8 rows (10.67% of the data) were excluded due to missing values.
  
  
  == testthat results  ===========================================================
  OK: 61 SKIPPED: 1 FAILED: 1
  1. Failure: A message is returned if some rows are missing (@test_missingValuesHandling.R#47) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [215s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(BMSC)
  Loading required package: Rcpp
  > 
  > test_check("BMSC")
  -- 1. Failure: A message is returned if some rows are missing (@test_missingValu
  `BMSC:::handleMissingData(data, formula, yUncertainty)$data` produced unexpected messages.
  Expected match: 7 rows \\(9.33% of the data\\) were excluded due to missing values.
  Actual values:
  * 8 rows (10.67% of the data) were excluded due to missing values.
  
  
  == testthat results  ===========================================================
  OK: 61 SKIPPED: 1 FAILED: 1
  1. Failure: A message is returned if some rows are missing (@test_missingValuesHandling.R#47) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/BonEV.Rcheck/00install.out' for details.
installed size is 83.9Mb
  sub-directories of 1Mb or more:
    include   3.1Mb
    lib      80.4Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
File 'brainwaver/libs/i386/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.o'
File 'brainwaver/libs/x64/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R     2.9Mb
    doc   1.8Mb
Foreign function calls to a different package:
  .C("CharArray", ..., PACKAGE = "libOpenBUGS")
  .C("CmdInterpreter", ..., PACKAGE = "libOpenBUGS")
  .C("Integer", ..., PACKAGE = "libOpenBUGS")
  .C("RealArray", ..., PACKAGE = "libOpenBUGS")
  .C("SetTempDir", ..., PACKAGE = "libOpenBUGS")
  .C("SetWorkingDir", ..., PACKAGE = "libOpenBUGS")
Undeclared package in foreign function calls:
   'libOpenBUGS'
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Package which this enhances but not available for checking: 'FastRWeb'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R        1.1Mb
    data     1.5Mb
    models   2.4Mb
Running 'testthat.R' [73s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(caret)
  Loading required package: lattice
  Loading required package: ggplot2
  > 
  > test_check("caret")
  -- 1. Failure: twoClassSummary is calculating correctly (@test_twoClassSummary.R
  mod1$resample$ROC not equal to mod2$resample$ROC.
  2/25 mismatches (average diff: 0.0045)
  [18] 0.836 - 0.831 ==  0.00529
  [21] 0.537 - 0.541 == -0.00370
  
  == testthat results  ===========================================================
  OK: 105 SKIPPED: 32 FAILED: 1
  1. Failure: twoClassSummary is calculating correctly (@test_twoClassSummary.R#31) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [80s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(caret)
  Loading required package: lattice
  Loading required package: ggplot2
  > 
  > test_check("caret")
  -- 1. Failure: twoClassSummary is calculating correctly (@test_twoClassSummary.R
  mod1$resample$ROC not equal to mod2$resample$ROC.
  2/25 mismatches (average diff: 0.0045)
  [18] 0.836 - 0.831 ==  0.00529
  [21] 0.537 - 0.541 == -0.00370
  
  == testthat results  ===========================================================
  OK: 105 SKIPPED: 32 FAILED: 1
  1. Failure: twoClassSummary is calculating correctly (@test_twoClassSummary.R#31) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   1.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/ccrs.Rcheck/00install.out' for details.
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(cctools)
  > 
  > test_check("cctools")
  -- 1. Failure: Simulation works (@test-usb.R#28)  ------------------------------
  max(abs(rusb(500, quasi = TRUE, theta = 0.99, nu = 1))) is not strictly more than 0.95. Difference: -0.000409
  
  == testthat results  ===========================================================
  OK: 36 SKIPPED: 1 FAILED: 1
  1. Failure: Simulation works (@test-usb.R#28) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.7Mb
    libs   2.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   2.2Mb
Running examples in 'CLA-Ex.R' failed
The error most likely occurred in:

> ### Name: findMu
> ### Title: Find mu(W) and W, given sigma(W) and CLA result
> ### Aliases: findMu
> ### Keywords: optimize arith
> 
> ### ** Examples
> 
> data(muS.sp500)
> ## Full data taking too much time for example
> set.seed(2016)
> iS <- sample.int(length(muS.sp500$mu), 17)
> cov17 <- muS.sp500$covar[iS, iS]
> CLsp.17 <- CLA(muS.sp500$mu[iS], covar=cov17, lB=0, uB = 1/2)
> CLsp.17 # 16 turning points
Call: CLA(mu = muS.sp500$mu[iS], covar = cov17, lB = 0, uB = 1/2)
Critical Line Algorithm for n = 17 assets, resulting in  17  turning points
Overview of result parts:
List of 5
 $ weights_set : num [1:17, 1:17] 0 0 0 0 0 0.5 0 0 0 0 ...
 $ free_indices:List of 17
 $ gammas      : num [1:17] NA -0.01915 -0.01915 -0.01018 -0.00242 ...
 $ lambdas     : num [1:17] NA 3.242 3.242 1.884 0.519 ...
 $ MS_weights  : num [1:17, 1:2] 0.0395 0.0395 0.0395 0.0395 0.0256 ...
> summary(tpS <- CLsp.17$MS_weights[,"Sig"])
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
0.01673 0.01768 0.02042 0.02421 0.02555 0.03946 
> str(s0 <- seq(0.0186, 0.0477, by = 0.0001))
 num [1:292] 0.0186 0.0187 0.0188 0.0189 0.019 0.0191 0.0192 0.0193 0.0194 0.0195 ...
> mu.. <- findMu(s0, result=CLsp.17, covar=cov17)
Error in FUN(X[[i]], ...) : Sig0 must be in [0.0167274, 0.0394623]
Calls: findMu -> lapply -> FUN
Execution halted
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(clhs)
  > 
  > test_check("clhs")
  -- 1. Failure: basic clhs on a data.frame works (@test-clhs-data.frame.R#15)  --
  `res` not equal to c(188, 657, 140, 301, 817).
  5/5 mismatches (average diff: 210)
  [1]  97 - 188 == -91
  [2] 903 - 657 == 246
  [3] 539 - 140 == 399
  [4] 451 - 301 == 150
  [5] 979 - 817 == 162
  
  -- 2. Failure: DLHS method on a data.frame works (@test-method_DLHS.R#17)  -----
  `res` not equal to c(214, 40, 702, 919, 521).
  5/5 mismatches (average diff: 211)
  [1] 412 - 214 ==  198
  [2] 170 -  40 ==  130
  [3] 196 - 702 == -506
  [4] 820 - 919 ==  -99
  [5] 641 - 521 ==  120
  
  == testthat results  ===========================================================
  OK: 4 SKIPPED: 0 FAILED: 2
  1. Failure: basic clhs on a data.frame works (@test-clhs-data.frame.R#15) 
  2. Failure: DLHS method on a data.frame works (@test-method_DLHS.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   1.9Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    pdf   2.2Mb
Package suggested but not available for checking: 'moe430a.db'
Running examples in 'CoDiNA-Ex.R' failed
The error most likely occurred in:

> ### Name: as.igraph
> ### Title: as.igraph
> ### Aliases: as.igraph
> 
> ### ** Examples
> 
> Nodes = LETTERS[1:10]
> Net1 = data.frame(Node.1 = sample(Nodes) , Node.2 = sample(Nodes), wTO = runif(10,-1,1))
> Net2 = data.frame(Node.1 = sample(Nodes) , Node.2 = sample(Nodes), wTO = runif(10,-1,1))
> Net3 = data.frame(Node.1 = sample(Nodes) , Node.2 = sample(Nodes), wTO = runif(10,-1,1))
> DiffNet = MakeDiffNet (Data = list(Net1,Net2,Net3), Code = c('Net1', 'Net2', 'Net3') )
Starting now.
Net1 contains 10 edges and 10 nodes.
Net2 contains 10 edges and 10 nodes.
Net3 contains 10 edges and 10 nodes.
Warning in CreateFullBase(x = Data, Code = Code) :
  You have duplicated links. Results will be presented, but you should double check your input.
Total of nodes: 10
Total of edges: 23
Coding correlations.
Total of edges (inside the cutoff): 13
Starting Phi categorization.
Coding the groups.
Recode is done!
> Graph = plot(x = DiffNet,
+  layout = NULL, smooth.edges = TRUE,
+  path = NULL, MakeGroups = FALSE, Cluster = FALSE,
+  legend = TRUE, manipulation = FALSE, sort.by.Phi = FALSE)
> x = as.igraph(Graph)
> 
> plot(x)
Error in plot.window(...) : need finite 'xlim' values
Calls: plot ... plot.igraph -> plot -> plot.default -> localWindow -> plot.window
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       2.2Mb
    extdata   2.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   5.0Mb
Package suggested but not available for checking: 'ProData'
Found the following significant warnings:
  Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
See 'd:/Rcompile/CRANpkg/local/3.6/CorrectOverloadedPeaks.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.3Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    shp   7.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   4.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.9Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
File 'curl/libs/i386/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'
File 'curl/libs/x64/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(cusum)
  > 
  > test_check("cusum")
  -- 1. Failure: Output of Control limit simulation (@test-racusum.R#21)  --------
  `result` not equal to `expected_results`.
  4/10 mismatches (average diff: 0.893)
  [7]  0.00 - 0.51 == -0.51
  [8]  0.00 - 1.02 == -1.02
  [9]  0.60 - 1.53 == -0.93
  [10] 0.42 - 1.53 == -1.11
  
  -- 2. Failure: Output of alpha simulation (@test-racusum_alpha_sim.R#20)  ------
  `works` not equal to `expected_results`.
  1/1 mismatches
  [1] 0.023 - 0.025 == -0.002
  
  -- 3. Failure: Output of Control limit simulation (@test_racusum_limit_sim.R#19)
  `works` not equal to `expected_results`.
  1/1 mismatches
  [1] 2.45 - 2.59 == -0.14
  
  == testthat results  ===========================================================
  OK: 3 SKIPPED: 0 FAILED: 3
  1. Failure: Output of Control limit simulation (@test-racusum.R#21) 
  2. Failure: Output of alpha simulation (@test-racusum_alpha_sim.R#20) 
  3. Failure: Output of Control limit simulation (@test_racusum_limit_sim.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(cvar)
  > 
  > test_check("cvar")
  -- 1. Failure: garch1c1 related functions work ok (@test-garch.R#24)  ----------
  `a_pred` has changed from known value recorded in 'a_pred.RDS'.
  Component "dist_sim": Component "RNGstate": Attributes: < Component "kind": Length mismatch: comparison on first 2 components >
  
  == testthat results  ===========================================================
  OK: 21 SKIPPED: 0 FAILED: 1
  1. Failure: garch1c1 related functions work ok (@test-garch.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   1.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.1Mb
Running examples in 'D2C-Ex.R' failed
The error most likely occurred in:

> ### Name: predict,D2C-method
> ### Title: predict if there is a connection between node i and node j
> ### Aliases: predict,D2C-method
> 
> ### ** Examples
> 
> require(RBGL)
Loading required package: RBGL
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 object is masked from 'package:randomForest':

    combine

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

> require(gRbase)
Loading required package: gRbase
> require(foreach)
Loading required package: foreach
> data(example)
> ## load the D2C object
> testDAG<-new("simulatedDAG",NDAG=1, N=50,noNodes=5,
+            functionType = "linear", seed=1,sdn=c(0.25,0.5))
simulatedDAG: DAG number: 1 generated: #nodes= 5 # edges= 0 # samples= 50 
> ## creates a simulatedDAG object for testing
> plot(testDAG@list.DAGs[[1]])
Error in testDAG@list.DAGs[[1]] : subscript out of bounds
Calls: plot
Execution halted
Running 'testthat.R' [28s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(DataExplorer)
  > 
  > test_check("DataExplorer")
  -- 1. Failure: .ignoreCat (@test-internal.r#11)  -------------------------------
  as.numeric(.ignoreCat(dt, 0)) not equal to c(1L, 2L, 5L, 10L).
  1/4 mismatches
  [3] 4 - 5 == -1
  
  -- 2. Failure: .ignoreCat (@test-internal.r#12)  -------------------------------
  as.numeric(.ignoreCat(dt, 1)) not equal to c(2L, 5L, 10L).
  1/3 mismatches
  [2] 4 - 5 == -1
  
  -- 3. Failure: .ignoreCat (@test-internal.r#13)  -------------------------------
  as.numeric(.ignoreCat(dt, 2)) not equal to c(5L, 10L).
  1/2 mismatches
  [1] 4 - 5 == -1
  
  == testthat results  ===========================================================
  OK: 130 SKIPPED: 7 FAILED: 3
  1. Failure: .ignoreCat (@test-internal.r#11) 
  2. Failure: .ignoreCat (@test-internal.r#12) 
  3. Failure: .ignoreCat (@test-internal.r#13) 
  
  Error: testthat unit tests failed
  Execution halted
.onLoad : <anonymous>: no visible global function definition for
  'read.table'
.onLoad : <anonymous>: no visible global function definition for
  'dbConnect'
.onLoad : <anonymous>: no visible global function definition for
  'dbListTables'
.onLoad : <anonymous>: no visible global function definition for
  'dbExistsTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbReadTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbWriteTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbDisconnect'
.onLoad : <anonymous>: no visible global function definition for
  'dbRemoveTable'
Undefined global functions or variables:
  dbConnect dbDisconnect dbExistsTable dbListTables dbReadTable
  dbRemoveTable dbWriteTable read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   5.0Mb
browse: no visible global function definition for 'slot'
browse: no visible global function definition for 'page'
default.options: no visible binding for global variable 'object.size'
heat.view: no visible global function definition for 'head'
heat.view: no visible global function definition for 'tail'
whos: no visible global function definition for 'slotNames'
whos : <anonymous> : <anonymous>: no visible global function definition
  for 'slot'
Undefined global functions or variables:
  head object.size page slot slotNames tail
Consider adding
  importFrom("methods", "slot", "slotNames")
  importFrom("utils", "head", "object.size", "page", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.3Mb
Running examples in 'DCD-Ex.R' failed
The error most likely occurred in:

> ### Name: DCD
> ### Title: Differential Community Detection for Paired Biological Networks,
> ###   for e.g. case vs control
> ### Aliases: DCD
> 
> ### ** Examples
> 
> 
> DCD_output <- DCD()
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
> ## Not run: 
> ##D library(igraph)
> ##D g_A <- sample_grg(200, 0.15, torus=FALSE, coords = FALSE)
> ##D g_B <- permute(g_A,c(sample(20),21:200))
> ##D ground_truth <- c(rep(1,20),rep(0,180))
> ##D DCD_output2 <- DCD(g_A = g_A, g_B = g_B, method = "Spectral", mink = 7,
> ##D                    ground_truth = ground_truth, plot_flag = 1, color = "red",
> ##D                    iter = 1, cores = 1 )
> ##D   
> ## End(Not run)
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11655 (sockconn)
Execution halted
Running examples in 'DCEM-Ex.R' failed
The error most likely occurred in:

> ### Name: dcem_train
> ### Title: dcem_train: Part of DCEM package.
> ### Aliases: dcem_train
> 
> ### ** Examples
> 
> # Simulating a mixture of univariate samples from three distributions
> # with mean as 20, 70 and 100 and standard deviation as 10, 100 and 40 respectively.
> sample_uv_data = as.data.frame(c(rnorm(1000, 20, 10), rnorm(500, 70, 100),
+ rnorm(2000, 100, 40)), row=3500)
Warning in as.data.frame.numeric(c(rnorm(1000, 20, 10), rnorm(500, 70, 100),  :
  'row.names' is not a character vector of length 3500 -- omitting it. Will be an error!
> 
> # Randomly shuffle the samples.
> sample_uv_data = as.data.frame(sample_uv_data[sample(1:nrow(sample_uv_data)),],
+ row=nrow(sample_uv_data))
Warning in as.data.frame.numeric(sample_uv_data[sample(1:nrow(sample_uv_data)),  :
  'row.names' is not a character vector of length 3500 -- omitting it. Will be an error!
> 
> # Calling the dcem_train() function on the simulated data with threshold of
> # 0.000001 and iteration count of 1000 respectively.
> sample_uv_out = dcem_train(sample_uv_data, num_clusters = 3, iteration_count = 1000,
+ threshold = 0.000001)
Error in if (mean_diff < threshold) { : 
  missing value where TRUE/FALSE needed
Calls: dcem_train -> dcem_cluster_uv
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
.makeICCDialog: no visible global function definition for 'J'
.makeICCDialog: no visible global function definition for 'new'
.makeICCDialog: no visible global function definition for '.jnull'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'new'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'J'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'toJava'
.makeNewLDADialog: no visible global function definition for 'new'
.makeNewLDADialog: no visible global function definition for 'J'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'new'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'toJava'
.makeNewLDADialog: no visible global function definition for 'toJava'
.makeNewReliabilityDialog: no visible global function definition for
  'new'
.makeNewReliabilityDialog: no visible global function definition for
  'toJava'
.onLoad: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for 'winMenuAdd'
.onLoad: no visible global function definition for 'winMenuAddItem'
.onLoad: no visible global function definition for 'jgr.getMenuNames'
.onLoad: no visible global function definition for 'jgr.insertMenu'
.onLoad: no visible global function definition for 'jgr.addMenu'
.onLoad: no visible global function definition for 'jgr.addMenuItem'
Undefined global functions or variables:
  .jnull J jgr.addMenu jgr.addMenuItem jgr.getMenuNames jgr.insertMenu
  new toJava winMenuAdd winMenuAddItem
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "winMenuAdd", "winMenuAddItem")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in 'degenes-Ex.R' failed
The error most likely occurred in:

> ### Name: deg
> ### Title: Detection of differentially expressed genes.
> ### Aliases: deg
> 
> ### ** Examples
> 
> X1 = matrix(rnorm(2000, 0, 1), 200, 10)
> X2 = matrix(rnorm(2000, 0, 1), 200, 10)
> index = sample(1:200, 5, replace=FALSE)
> X2[index,] = X2[index,] + 5
> D = deg(X1, X2)
Sat Mar 02 01:37:01 2019
Calculation of Z
Calculation of z
Calculation of the kernel estimator
Calculation of the kernel estimator
Determination of the rejection region
Error in if (integral > single.alpha) c1 <- c : 
  missing value where TRUE/FALSE needed
Calls: deg
Execution halted
Running examples in 'deisotoper-Ex.R' failed
The error most likely occurred in:

> ### Name: deisotope
> ### Title: Deisotope a Mass Spectrum
> ### Aliases: deisotope
> 
> ### ** Examples
> 
> 
> x <- list(mZ = c(1, 2, 2.5, 3), intensity = rep(1, 4), pepmass=600, charge=2)
> 
> xd <- deisotope(dtoper <- deisotoper(), x)
> plot.deisotoper(x, xd)
> summary(dtoper)
  NumberOfIsotopicSets NumberOfIsotopicClusters NumberOfPeaksInIsotopicClusters
1                    1                        2                               4
  NumberOfPeaks
1             4
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	Summary (textConnection)
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Bootstrapping.CI: no visible global function definition for 'quantile'
D.Jost: no visible global function definition for 'read.table'
D.Jost: no visible global function definition for 'write.table'
Dv.locis.corrected.calc: no visible global function definition for
  'p.adjust'
Gst.Nei: no visible global function definition for 'read.table'
Gst.Nei: no visible global function definition for 'write.table'
H.out: no visible global function definition for 'write.table'
Hardy.calc: no visible global function definition for 'chisq.test'
critical.ci.values: no visible global function definition for
  'quantile'
inputformat: no visible global function definition for 'read.table'
inputformat: no visible global function definition for 'write.table'
over.all.pops: no visible global function definition for 'write.table'
p.value.correcture: no visible global function definition for
  'p.adjust'
pair.pops: no visible global function definition for 'write.table'
Undefined global functions or variables:
  chisq.test p.adjust quantile read.table write.table
Consider adding
  importFrom("stats", "chisq.test", "p.adjust", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.6Mb
    help   1.4Mb
    libs   2.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.8Mb
Running examples in 'dgmb-Ex.R' failed
The error most likely occurred in:

> ### Name: dgmb-package
> ### Title: Simulating Data for PLS Mode B Structural Models
> ### Aliases: dgmb-package dgmb
> ### Keywords: package
> 
> ### ** Examples
> 
> dgmbGui()
 --------------------------------------------------
| Simulating Data for PLS Mode B Structural Models |
| Version: 1.2                                     |
| Depends: abind, tcltk, MASS                      |
| Licence: GPL >= 2                                |
| System Requirements: tktable, BWidget            |
 --------------------------------------------------
Warning in tclRequire("Tktable") : Tcl package 'Tktable' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "table".
Calls: dgmbGui -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
Running examples in 'DiffNet-Ex.R' failed
The error most likely occurred in:

> ### Name: diffnet
> ### Title: Detection of Statistically Significant Changes in Paired
> ###   Biological Networks
> ### Aliases: diffnet
> 
> ### ** Examples
> 
> library("DiffNet")
> # this step is optional, it helps speed up calculations, run in parallel on 2 processors
> library(doParallel)
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> registerDoParallel(2)
> # Run the differential network analysis tehcnique on sample data
> p <- diffnet()
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11394 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11394 (sockconn)
Execution halted
Running examples in 'DiffNet-Ex.R' failed
The error most likely occurred in:

> ### Name: diffnet
> ### Title: Detection of Statistically Significant Changes in Paired
> ###   Biological Networks
> ### Aliases: diffnet
> 
> ### ** Examples
> 
> library("DiffNet")
> # this step is optional, it helps speed up calculations, run in parallel on 2 processors
> library(doParallel)
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> registerDoParallel(2)
> # Run the differential network analysis tehcnique on sample data
> p <- diffnet()
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11616 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11616 (sockconn)
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    5.1Mb
    libs   1.4Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    5.6Mb
    libs   1.4Mb
Output for data("exHartigan"):
  'exHartigan' data is identical to 'statfaculty' and hence deprecated.
   Use the 'statfaculty' instead
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(disclapmix)
  > 
  > test_check("disclapmix")
  -- 1. Failure: simulate (@test-disclapmix.R#152)  ------------------------------
  sim_fit$disclap_parameters not equal to fit_std_int_coef$disclap_parameters.
  5/6 mismatches (average diff: 0.139)
  [1] 0.326 - 0.453 == -0.127
  [2] 0.454 - 0.311 ==  0.142
  [4] 0.337 - 0.224 ==  0.113
  [5] 0.364 - 0.540 == -0.176
  [6] 0.506 - 0.371 ==  0.135
  
  -- 2. Failure: simulate (@test-disclapmix.R#153)  ------------------------------
  sim_fit$y not equal to fit_std_int_coef$y.
  4/6 mismatches (average diff: 1.5)
  [3] 20 - 19 ==  1
  [4] 19 - 20 == -1
  [5] 22 - 20 ==  2
  [6] 20 - 22 == -2
  
  -- 3. Failure: rcpp_find_haplotype_in_matrix (@test-disclapmix.R#209)  ---------
  33 not equal to find_haplotype_in_matrix(x, x[33L, ]).
  1/1 mismatches
  [1] 33 - 1 == 32
  
  == testthat results  ===========================================================
  OK: 50 SKIPPED: 0 FAILED: 3
  1. Failure: simulate (@test-disclapmix.R#152) 
  2. Failure: simulate (@test-disclapmix.R#153) 
  3. Failure: rcpp_find_haplotype_in_matrix (@test-disclapmix.R#209) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(disclapmix)
  > 
  > test_check("disclapmix")
  -- 1. Failure: simulate (@test-disclapmix.R#152)  ------------------------------
  sim_fit$disclap_parameters not equal to fit_std_int_coef$disclap_parameters.
  5/6 mismatches (average diff: 0.139)
  [1] 0.326 - 0.453 == -0.127
  [2] 0.454 - 0.311 ==  0.142
  [4] 0.337 - 0.224 ==  0.113
  [5] 0.364 - 0.540 == -0.176
  [6] 0.506 - 0.371 ==  0.135
  
  -- 2. Failure: simulate (@test-disclapmix.R#153)  ------------------------------
  sim_fit$y not equal to fit_std_int_coef$y.
  4/6 mismatches (average diff: 1.5)
  [3] 20 - 19 ==  1
  [4] 19 - 20 == -1
  [5] 22 - 20 ==  2
  [6] 20 - 22 == -2
  
  -- 3. Failure: rcpp_find_haplotype_in_matrix (@test-disclapmix.R#209)  ---------
  33 not equal to find_haplotype_in_matrix(x, x[33L, ]).
  1/1 mismatches
  [1] 33 - 1 == 32
  
  == testthat results  ===========================================================
  OK: 50 SKIPPED: 0 FAILED: 3
  1. Failure: simulate (@test-disclapmix.R#152) 
  2. Failure: simulate (@test-disclapmix.R#153) 
  3. Failure: rcpp_find_haplotype_in_matrix (@test-disclapmix.R#209) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/distrEllipse.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    include  15.9Mb
    libs      1.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   2.1Mb
    libs   2.0Mb
Error(s) in re-building vignettes:
--- re-building 'EDA.Rmd' using rmarkdown

Attaching package: 'dlookr'

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

    transform


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 167-170 (EDA.Rmd) 
Error: processing vignette 'EDA.Rmd' failed with diagnostics:
Need at least 4 complete observations.
--- failed re-building 'EDA.Rmd'

--- re-building 'diagonosis.Rmd' using rmarkdown

Attaching package: 'dlookr'

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

    transform


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

Loading required package: DBI
Loading required package: RSQLite
Loading required package: dbplyr

Attaching package: 'dbplyr'

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

    ident, sql

--- finished re-building 'diagonosis.Rmd'

--- re-building 'transformation.Rmd' using rmarkdown

Attaching package: 'dlookr'

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

    transform


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 'transformation.Rmd'

SUMMARY: processing the following file failed:
  'EDA.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'rPython'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.2Mb
Error: package or namespace load failed for 'dpcR' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called 'mvtnorm'
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
Error: package or namespace load failed for 'dpcR' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called 'mvtnorm'
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
Error: package or namespace load failed for 'dpcR' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called 'mvtnorm'
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   6.6Mb
File 'DPpackage/libs/i386/DPpackage.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Objects: 'DPdensityreg.o', 'LDBDPdensity.o', 'LDDPdensity.o',
      'LDDPsurvival.o', 'LDPDdoublyintsba.o', 'LDTFPdensity.o',
      'LDTFPglmmpois.o', 'LDTFPsurvival.o', 'PSgamgam.o',
      'PSgamgauss.o', 'PSgamlogit.o', 'PSgampois.o', 'PSgamprob.o',
      'ToolsLDTFP.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Objects: 'DPdensityreg.o', 'LDBDPdensity.o', 'LDDPdensity.o',
      'LDDPsurvival.o', 'LDPDdoublyintsba.o', 'LDTFPdensity.o',
      'LDTFPglmmpois.o', 'LDTFPsurvival.o', 'PSgamgam.o',
      'PSgamgauss.o', 'PSgamlogit.o', 'PSgampois.o', 'PSgamprob.o',
      'ToolsLDTFP.o'
File 'DPpackage/libs/x64/DPpackage.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Objects: 'DPdensityreg.o', 'LDBDPdensity.o', 'LDDPdensity.o',
      'LDDPsurvival.o', 'LDPDdoublyintsba.o', 'LDTFPdensity.o',
      'LDTFPglmmpois.o', 'LDTFPsurvival.o', 'PSgamgam.o',
      'PSgamgauss.o', 'PSgamlogit.o', 'PSgampois.o', 'PSgamprob.o',
      'ToolsLDTFP.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Objects: 'DPdensityreg.o', 'LDBDPdensity.o', 'LDDPdensity.o',
      'LDDPsurvival.o', 'LDPDdoublyintsba.o', 'LDTFPdensity.o',
      'LDTFPglmmpois.o', 'LDTFPsurvival.o', 'PSgamgam.o',
      'PSgamgauss.o', 'PSgamlogit.o', 'PSgampois.o', 'PSgamprob.o',
      'ToolsLDTFP.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Error: package or namespace load failed for 'drLumi' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'mvtnorm'
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
Error: package or namespace load failed for 'drLumi' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'mvtnorm'
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Error: package or namespace load failed for 'drLumi' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'mvtnorm'
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
Error: package or namespace load failed for 'drLumi' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'mvtnorm'
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called 'mvtnorm'
Calls: <Anonymous>
Execution halted
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    appinformation   9.6Mb
    media            1.2Mb
Running examples in 'DTRlearn-Ex.R' failed
The error most likely occurred in:

> ### Name: Olearning_Single
> ### Title: Improved single stage O-learning with cross validation
> ### Aliases: Olearning_Single
> 
> ### ** Examples
> 
> n_cluster=5
> pinfo=10
> pnoise=10
> n_sample=50
> set.seed(3)
> example=make_classification(n_cluster,pinfo,pnoise,n_sample)
> pi=list()
> pi[[2]]=pi[[1]]=rep(1,n_sample)
> modelrbf=Olearning_Single(example$X,example$A,example$R,kernel='rbf',m=3,sigma=0.05)
[1] 0.5
[1] NA
Error in svd(rbind(rho, tau, matrix(alpha), nu)) : 
  infinite or missing values in 'x'
Calls: Olearning_Single -> wsvm -> ipop -> ipop -> svd
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.1Mb
Running 'testthat.R' [99s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(dtwclust)
  Loading required package: proxy
  
  Attaching package: 'proxy'
  
  The following objects are masked from 'package:stats':
  
      as.dist, dist
  
  The following object is masked from 'package:base':
  
      as.matrix
  
  Loading required package: dtw
  Loaded dtw v1.20-1. See ?dtw for help, citation("dtw") for use in publication.
  
  dtwclust:
  Setting random number generator to L'Ecuyer-CMRG (see RNGkind()).
  To read the included vignettes type: browseVignettes("dtwclust").
  See news(package = "dtwclust") after package updates.
  > library(foreach)
  > library(testthat)
  > 
  > # coverage for multi-threading might not be possible (?)
  > if (nzchar(Sys.getenv("R_COVR"))) RcppParallel::setThreadOptions(1L)
  > # old reporter for CMD checks
  > options(testthat.default_reporter = "summary")
  > 
  > #' To test in a local machine:
  > #' Sys.setenv(NOT_CRAN = "true"); test_dir("tests/testthat/")
  > #' OR
  > #' devtools::test() # broken, can't figure out why
  > #'
  > #' To disable parallel tests, before calling test() run:
  > #'
  > #'   options(dtwclust_skip_par_tests = TRUE)
  > #'
  > testthat::test_check("dtwclust")
  -- 1. Failure: Cluster reinitialization in partitional tsclust works.  ---------
  `... <- NULL` did not produce any warnings.
  
  -- 2. Failure: Cluster reinitialization in partitional tsclust works.  ---------
  pc_cr@converged isn't false.
  
  == testthat results  ===========================================================
  OK: 1889 SKIPPED: 3 FAILED: 2
  1. Failure: Cluster reinitialization in partitional tsclust works. 
  2. Failure: Cluster reinitialization in partitional tsclust works. 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    2.5Mb
    libs   4.8Mb
Running examples in 'DZEXPM-Ex.R' failed
The error most likely occurred in:

> ### Name: dzexpm
> ### Title: The estimation and prediction function for the skewed spatial
> ###   processes
> ### Aliases: dzexpm
> 
> ### ** Examples
> 
>   real<- as.matrix(do.call(cbind, MaxTemp03))
>   n_ful<- nrow(real)
>   y_ful<- real[,2]
>   x_ful<- real[,7]
>   x_ful<- log(x_ful)
>   x_ful<- scale(x_ful)
>   u1<- real[,3]
>   u2<- real[,4]
>   theta<- 2/150000
>   n<- 56
>   p<- 0.1
>  dzexpm(y_ful, x_ful, n_ful, n, u1, u2, theta, p, 50, 20)
Error in chol.default(Cpred) : 
  the leading minor of order 19 is not positive definite
Calls: dzexpm -> t -> chol -> chol.default
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    hac    4.0Mb
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(edfReader)
  > 
  > test_check("edfReader")
  edfPlusC.edf : Testing header
  edfPlusC.edf : Testing signals
  bdfPlusC.bdf : Testing header
  bdfPlusC.bdf : Testing signals
  edfAnnonC.edf : Testing header
  edfAnnonC.edf : Testing signals
  edfPlusD.edf : Testing header
  edfPlusD.edf : Testing signals
  testASignalsFile edfPlusC.edf 
  testASignalsFile bdfPlusC.bdf 
  testASignalsFile edfPlusD.edf 
  testASignalsFile edfAnnonC.edf 
  -- 1. Failure: A6: A random range 3 (@test20_FromTill.R#162)  ------------------
  aSignal$annotations not equal to allAnnots[annotsInRange, ].
  Attributes: < Component "row.names": Mean relative difference: 0.6666667 >
  
  edfPlusC.edf : testOSignalsFile: isContinuous= TRUE 
  bdfPlusC.bdf : testOSignalsFile: isContinuous= TRUE 
  edfPlusD.edf : testOSignalsFile: isContinuous= FALSE 
  edfAnnonC.edf : testOSignalsFile: isContinuous= TRUE 
  edfPlusC.edf : min/max tests
  bdfPlusC.bdf : min/max tests
  edfPlusD.edf : min/max tests
  edfAnnonC.edf : min/max tests
  edfPlusC.edf : signal selection tests
  bdfPlusC.bdf : signal selection tests
  edfPlusD.edf : signal selection tests
  edfAnnonC.edf : signal selection tests
  == testthat results  ===========================================================
  OK: 790 SKIPPED: 0 FAILED: 1
  1. Failure: A6: A random range 3 (@test20_FromTill.R#162) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'test-all.R' [17s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > library(eeptools)
  Loading required package: ggplot2
  > 
  > test_check("eeptools")
  -- 1. Failure: statamode returns correct modes for each method using numbers (@t
  `d` not equal to 4.
  1/1 mismatches
  [1] 7 - 4 == 3
  
  -- 2. Failure: statamode handles all types of modes (@test-statamode.r#128)  ---
  statamode(vecA, method = tests[i, "method"]) not equal to "B".
  1/1 mismatches
  x[1]: "F"
  y[1]: "B"
  
  == testthat results  ===========================================================
  OK: 517 SKIPPED: 0 FAILED: 2
  1. Failure: statamode returns correct modes for each method using numbers (@test-statamode.r#24) 
  2. Failure: statamode handles all types of modes (@test-statamode.r#128) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
prepare_Rd: index.egonet.Rd:29-31: Dropping empty section \details
prepare_Rd: index.egonet.Rd:32-38: Dropping empty section \value
prepare_Rd: index.egonet.Rd:45-47: Dropping empty section \note
prepare_Rd: index.egonet.Rd:39-41: Dropping empty section \references
prepare_Rd: index.egonet.Rd:51-53: Dropping empty section \seealso
prepare_Rd: read.egonet.Rd:27-29: Dropping empty section \note
Running examples in 'egonet-Ex.R' failed
The error most likely occurred in:

> ### Name: egonet-package
> ### Title: Tool for ego-centric measures in Social Network Analysis
> ### Aliases: egonet-package egonet
> ### Keywords: package
> 
> ### ** Examples
> 
> ## This is a list of file' names containing the ego-network
> ff <- c("q1.csv","q2.csv","q3.csv")
> files  <- paste("http://www.egonet.associazionerospo.org/egonetdata/",ff,sep="")
> names(files) <- ff
> 
> ##if all your data are in a directory (eg. egonets, containing all files with the same extension), 
> ##you can easily get this list with the following commands
> # ff <- dir("./egonets",pattern=".csv")
> # files  <- paste("./egonets/",ff,sep="")
> # names(files) <- ff
> 
> 
> # Here is a dataset with demographic informations and the names of files containing the ego-network
> #we now want to add network indeces to this data.frame
> data <- data.frame( gender=c("F","F","M"), age =(2:4)*10, filename=ff)
> data
  gender age filename
1      F  20   q1.csv
2      F  30   q2.csv
3      M  40   q3.csv
> 
> 
> #import all the egonets
> mats <- lapply(files,read.egonet)
Error in `[.data.frame`(dat, , ego.name) : undefined columns selected
Calls: lapply -> FUN -> [ -> [.data.frame -> [ -> [.data.frame
Execution halted
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(EGRETci)
  > test_check("EGRETci")
  -- 1. Failure: blockSample (@tests_boot_tests.R#72)  ---------------------------
  bsReturn$ConcLow[1] not equal to 0.62.
  1/1 mismatches
  [1] 1.4 - 0.62 == 0.78
  
  -- 2. Failure: blockSample (@tests_boot_tests.R#73)  ---------------------------
  bsReturn$Date[1] not equal to as.Date("1979-10-24").
  Mean relative difference: 0.01158621
  
  == testthat results  ===========================================================
  OK: 17 SKIPPED: 5 FAILED: 2
  1. Failure: blockSample (@tests_boot_tests.R#72) 
  2. Failure: blockSample (@tests_boot_tests.R#73) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'ellipticpaper.Rnw' using Sweave

Attaching package: 'elliptic'

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

    sd, sigma

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

    is.primitive

Loading required package: emulator
Loading required package: mvtnorm
Loading required package: calibrator

Error: processing vignette 'ellipticpaper.Rnw' failed with diagnostics:
 chunk 62 (label = mle_calc) 
Error in stats::optim(par = par, fn = fn, control = list(fnscale = -1)) : 
  function cannot be evaluated at initial parameters

--- failed re-building 'ellipticpaper.Rnw'

--- re-building 'residuetheorem.Rnw' using Sweave

Attaching package: 'elliptic'

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

    sd, sigma

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

    is.primitive

--- finished re-building 'residuetheorem.Rnw'

SUMMARY: processing the following file failed:
  'ellipticpaper.Rnw'

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
See 'd:/Rcompile/CRANpkg/local/3.6/EMA.Rcheck/00install.out' for details.
Running 'testthat.R' [16s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > if (packageVersion("testthat") >= "0.9.1") {
  +   library(testthat)
  +   test_check("emil")
  + }
  Loading required package: emil
  
  Attaching package: 'emil'
  
  The following object is masked from 'package:base':
  
      mode
  
  -- 1. Failure: k-NN imputation (@test-preprocess.r#30)  ------------------------
  sets$test$x[na.ind] not equivalent to ifelse(na.ind[, 2] <= 3, 5, 4.5).
  3/10 mismatches (average diff: 0.5)
  [5]  5 - 4.5 == 0.5
  [7]  5 - 4.5 == 0.5
  [10] 5 - 4.5 == 0.5
  
  == testthat results  ===========================================================
  OK: 179 SKIPPED: 1 FAILED: 1
  1. Failure: k-NN imputation (@test-preprocess.r#30) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > if (packageVersion("testthat") >= "0.9.1") {
  +   library(testthat)
  +   test_check("emil")
  + }
  Loading required package: emil
  
  Attaching package: 'emil'
  
  The following object is masked from 'package:base':
  
      mode
  
  -- 1. Failure: k-NN imputation (@test-preprocess.r#30)  ------------------------
  sets$test$x[na.ind] not equivalent to ifelse(na.ind[, 2] <= 3, 5, 4.5).
  3/10 mismatches (average diff: 0.5)
  [5]  5 - 4.5 == 0.5
  [7]  5 - 4.5 == 0.5
  [10] 5 - 4.5 == 0.5
  
  == testthat results  ===========================================================
  OK: 179 SKIPPED: 1 FAILED: 1
  1. Failure: k-NN imputation (@test-preprocess.r#30) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.3Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(fabricatr)
  > 
  > test_check("fabricatr")
  -- 1. Failure: Multi-level Resample validity (@test-resampling.R#155)  ---------
  length(unique(split(resample_validity$cities, rep(1:6, each = 5)))) not equal to 6.
  1/1 mismatches
  [1] 5 - 6 == -1
  
  == testthat results  ===========================================================
  OK: 363 SKIPPED: 1 FAILED: 1
  1. Failure: Multi-level Resample validity (@test-resampling.R#155) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.7Mb
File 'fastmatch/libs/i386/fastmatch.dll':
  Found non-API call to R: 'match5'
File 'fastmatch/libs/x64/fastmatch.dll':
  Found non-API call to R: 'match5'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/FastRWeb.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.0Mb
Running examples in 'fdapace-Ex.R' failed
The error most likely occurred in:

> ### Name: CreateBWPlot
> ### Title: Functional Principal Component Analysis Bandwidth Diagnostics
> ###   plot
> ### Aliases: CreateBWPlot
> 
> ### ** Examples
> 
> set.seed(1)
> n <- 20
> pts <- seq(0, 1, by=0.05)
> sampWiener <- Wiener(n, pts)
> sampWiener <- Sparsify(sampWiener, pts, 10)
> res1 <- FPCA(sampWiener$Ly, sampWiener$Lt, 
+             list(dataType='Sparse', error=FALSE, kernel='epan', verbose=FALSE))
> CreateBWPlot(res1)
Error in value[[3L]](cond) : 
  Multiplier : 0.5 failed to return valid FPCA object. Change multiplier values.
Calls: CreateBWPlot ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
    libs   1.7Mb
Packages suggested but not available for checking: 'doMC', 'RSvgDevice'
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R   6.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
Package which this enhances but not available for checking: 'doMC'
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs  10.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.6Mb
Package suggested but not available for checking: 'dggrids'
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    2.1Mb
    libs   1.4Mb
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(funData)
  
  Attaching package: 'funData'
  
  The following object is masked from 'package:stats':
  
      integrate
  
  > 
  > test_check("funData")
  -- 1. Failure: sparsify (@test_simulation.R#219)  ------------------------------
  nObsPoints(s) not equal to c(2, 2).
  1/2 mismatches
  [2] 3 - 2 == 1
  
  -- 2. Failure: sparsify (@test_simulation.R#220)  ------------------------------
  argvals(s) not equal to list(c(0.57, 0.7), c(0.94, 0.95)).
  Component 1: Mean relative difference: 0.1360544
  Component 2: Numeric: lengths (3, 2) differ
  
  -- 3. Failure: sparsify (@test_simulation.R#221)  ------------------------------
  X(s) not equal to list(c(1.17678, -2.76915), c(-2.40195, -2.32616)).
  Component 1: Mean relative difference: 0.7422477
  Component 2: Numeric: lengths (3, 2) differ
  
  -- 4. Failure: sparsify (@test_simulation.R#227)  ------------------------------
  as.irregFunData(s[[1]])@argvals not equal to list(4, 2).
  Component 1: Mean relative difference: 1
  Component 2: Numeric: lengths (2, 1) differ
  
  -- 5. Failure: sparsify (@test_simulation.R#228)  ------------------------------
  as.irregFunData(s[[1]])@X not equal to list(4, 3).
  Component 1: Mean relative difference: 1
  Component 2: Numeric: lengths (2, 1) differ
  
  == testthat results  ===========================================================
  OK: 488 SKIPPED: 0 FAILED: 5
  1. Failure: sparsify (@test_simulation.R#219) 
  2. Failure: sparsify (@test_simulation.R#220) 
  3. Failure: sparsify (@test_simulation.R#221) 
  4. Failure: sparsify (@test_simulation.R#227) 
  5. Failure: sparsify (@test_simulation.R#228) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'funHDDC-Ex.R' failed
The error most likely occurred in:

> ### Name: predict.funHDDC
> ### Title: Predict new results from a funHDDC model
> ### Aliases: predict.funHDDC
> 
> ### ** Examples
> 
> ##Univariate example
>     data("trigo")
>     basis<- create.bspline.basis(c(0,1), nbasis=25)
>     z<-sample(1:100,0.8*100,replace=FALSE)
>     var1_train<-smooth.basis(argvals=seq(0,1,length.out = 100),y=t(trigo[z,1:100]),
+                              fdParobj=basis)$fd
>     var1_test<-smooth.basis(argvals=seq(0,1,length.out = 100),y=t(trigo[-z,1:100]),
+                             fdParobj=basis)$fd
> 
>     model<-funHDDC(var1_train,K=2)
      model K threshold complexity         BIC
1 AKJBKQKDK 2       0.2        103 -373,867.94

SELECTED: model  AKJBKQKDK  with  2  clusters.
Selection Criterion: BIC.
>     pred<-predict(model,var1_test)
> 
> ##Multivariate example
>     data("triangle")
>     basis<- create.bspline.basis(c(1,21), nbasis=25)
>     z<-sample(1:100,0.8*100,replace=FALSE)
>     var1_train<-smooth.basis(argvals=seq(1,21,length.out = 101),y=t(triangle[z,1:101]),
+                               fdParobj=basis)$fd
>     var1_test<-smooth.basis(argvals=seq(1,21,length.out = 101),y=t(triangle[-z,1:101]),
+                             fdParobj=basis)$fd
>     var2_train<-smooth.basis(argvals=seq(1,21,length.out = 101),y=t(triangle[z,102:202]),
+                             fdParobj=basis)$fd
>     var2_test<-smooth.basis(argvals=seq(1,21,length.out = 101),y=t(triangle[-z,102:202]),
+                             fdParobj=basis)$fd
> 
>     model<-funHDDC(list(var1_train,var2_train),K=3)
Warning in funHDDC(list(var1_train, var2_train), K = 3) :
  All models diverged.
>     pred<-predict(model,list(var1_test,var2_test))
Error in UseMethod("predict") : 
  no applicable method for 'predict' applied to an object of class "list"
Calls: predict
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.5Mb
    libs      1.5Mb
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  5.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   2.7Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
Running 'test-all.R' [66s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > library(gastempt)
  > 
  > test_check("gastempt")
  -- 1. Failure: nlme_gastempt can handle noisy and missing data (@test-fitnlme.R#
  fit$message not equal to "Ok".
  1/1 mismatches
  x[1]: "pnlsTol =  0.62 \n Error in nlme.formula(vol ~ linexp(minute, v0, tempt, 
  x[1]: kappa), data = d,  : \n  maximum number of iterations (maxIter = 15) reach
  x[1]: ed without convergence\n"
  y[1]: "Ok"
  
  -- 2. Failure: nlme_gastempt with special data fails (@test-fitnlme.R#46)  -----
  fit$pnlsTol not equal to 0.001.
  1/1 mismatches
  [1] 0.125 - 0.001 == 0.124
  
  -- 3. Failure: fit of powexp data with beta=2 to linexp curve converges (@test-f
  fit$pnlsTol not equal to 0.001.
  1/1 mismatches
  [1] 0.625 - 0.001 == 0.624
  
  -- 4. Failure: fit of powexp data with beta=2 to linexp curve converges (@test-f
  fit$message not equal to "Ok".
  1/1 mismatches
  x[1]: "pnlsTol =  0.62 \n Error in nlme.formula(vol ~ linexp(minute, v0, tempt, 
  x[1]: kappa), data = d,  : \n  maximum number of iterations (maxIter = 15) reach
  x[1]: ed without convergence\n"
  y[1]: "Ok"
  
  
  Testing  linexp_gastro_1b 
  
  Testing  powexp_gastro_1b 
  == testthat results  ===========================================================
  OK: 221 SKIPPED: 10 FAILED: 4
  1. Failure: nlme_gastempt can handle noisy and missing data (@test-fitnlme.R#28) 
  2. Failure: nlme_gastempt with special data fails (@test-fitnlme.R#46) 
  3. Failure: fit of powexp data with beta=2 to linexp curve converges (@test-fitnlme.R#102) 
  4. Failure: fit of powexp data with beta=2 to linexp curve converges (@test-fitnlme.R#103) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'test-all.R' [50s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > library(gastempt)
  > 
  > test_check("gastempt")
  -- 1. Failure: nlme_gastempt can handle noisy and missing data (@test-fitnlme.R#
  fit$message not equal to "Ok".
  1/1 mismatches
  x[1]: "pnlsTol =  0.62 \n Error in nlme.formula(vol ~ linexp(minute, v0, tempt, 
  x[1]: kappa), data = d,  : \n  maximum number of iterations (maxIter = 15) reach
  x[1]: ed without convergence\n"
  y[1]: "Ok"
  
  -- 2. Failure: nlme_gastempt with special data fails (@test-fitnlme.R#46)  -----
  fit$pnlsTol not equal to 0.001.
  1/1 mismatches
  [1] 0.125 - 0.001 == 0.124
  
  
  Testing  linexp_gastro_1b 
  
  Testing  powexp_gastro_1b 
  == testthat results  ===========================================================
  OK: 223 SKIPPED: 10 FAILED: 2
  1. Failure: nlme_gastempt can handle noisy and missing data (@test-fitnlme.R#28) 
  2. Failure: nlme_gastempt with special data fails (@test-fitnlme.R#46) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      4.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.8Mb
Running examples in 'gcite-Ex.R' failed
The error most likely occurred in:

> ### Name: gcite_author_info
> ### Title: Getting User Information from name
> ### Aliases: gcite_author_info
> 
> ### ** Examples
> 
> ## Not run: 
> ##D if (!is_travis()) {
> ##D df = gcite_author_info(author = "John Muschelli", secure = FALSE)
> ##D }
> ## End(Not run)
> if (!is_travis()) {
+ df = gcite_author_info(author = "Jiawei Bai", secure = FALSE)
+ } 
Error in dat$fullnames[is.na(dat$insts)] <- dat$names[is.na(dat$insts)] : 
  replacement has length zero
Calls: gcite_author_info -> gcite_username
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   3.0Mb
    libs      1.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Running examples in 'genBaRcode-Ex.R' failed
The error most likely occurred in:

> ### Name: plotClusterGgTree
> ### Title: Plotting a Cluster ggTree
> ### Aliases: plotClusterGgTree
> 
> ### ** Examples
> 
> data(BC_dat)
> plotClusterGgTree(BC_dat, tree_est = "UPGMA", type = "circular")
Error: object 'as_data_frame' is not exported by 'namespace:tidytree'
Execution halted
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(httr)
  > library(genderizeR)
  
  Welcome to genderizeR package version: 2.0.0
  
  Homepage: http://www.wais.kamil.rzeszow.pl/genderizeR
  
  Changelog: news(package = 'genderizeR')
  Help & Contact: help(genderizeR)
  
  If you find this package useful cite it please. Thank you! 
  See: citation('genderizeR')
  
  To suppress this message use:
  suppressPackageStartupMessages(library(genderizeR))
  > 
  > test_check("genderizeR")
  -- 1. Failure: classificationErrors (@test.R#63)  ------------------------------
  ...$NULL not equal to 0.6521739.
  1/1 mismatches
  [1] 0.617 - 0.652 == -0.0352
  
  == testthat results  ===========================================================
  OK: 23 SKIPPED: 2 FAILED: 1
  1. Failure: classificationErrors (@test.R#63) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R         6.1Mb
    extdata   1.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
Running examples in 'ggdag-Ex.R' failed
The error most likely occurred in:

> ### Name: ggdag
> ### Title: Quickly plot a DAG in ggplot2
> ### Aliases: ggdag
> 
> ### ** Examples
> 
> 
> dag  <- dagify(y ~ x + z2 + w2 + w1,
+   x ~ z1 + w1,
+   z1 ~ w1 + v,
+   z2 ~ w2 + v,
+   w1 ~~ w2)
> 
> ggdag(dag)
> ggdag(dag) + theme_dag_blank()
> 
> ggdag(dagitty::randomDAG(5, .5))
Error in .f(.x[[i]], ...) : object 'v' not found
Calls: ggdag ... <Anonymous> -> vars_select_eval -> map_if -> map -> .f
Execution halted
Running 'test-all.R' [78s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > 
  > test_check('ggfortify')
  Loading required package: ggfortify
  Loading required package: ggplot2
  initial  value 7.505733 
  final  value 7.505688 
  converged
  Initial stress        : 0.01705
  stress after  10 iters: 0.00951, magic = 0.500
  stress after  20 iters: 0.00941, magic = 0.500
  initial  value 7.505733 
  final  value 7.505688 
  converged
  Initial stress        : 0.01705
  stress after  10 iters: 0.00951, magic = 0.500
  stress after  20 iters: 0.00941, magic = 0.500
  -- 1. Failure: fortify.glmnet works for Orange (@test-glmnet.R#33)  ------------
  dim(fortified) not equal to c(57, 5).
  1/2 mismatches
  [1] 56 - 57 == -1
  
  == testthat results  ===========================================================
  OK: 1451 SKIPPED: 9 FAILED: 1
  1. Failure: fortify.glmnet works for Orange (@test-glmnet.R#33) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'GGMM-Ex.R' failed
The error most likely occurred in:

> ### Name: BRGM
> ### Title: Learning gene regulatory networks for breast cancer.
> ### Aliases: BRGM
> ### Keywords: BRGM
> 
> ### ** Examples
> 
>  ## Don't show: 
> set.seed(10)
> library(GGMM)
> data(breast)
> Gra <- BRGM(breast[1:50,1:5], M=2,alpha1 = 0.5, alpha2 = 0.8, alpha3 = 0.9, iteration = 1, warm = 0)
working subdata size=10
Read 25 items
Read 30 items
working subdata size=10
The given q-threshold value is too small
Warning in file(file, "r") :
  cannot open file 'sim0.pcor.est.ini': No such file or directory
Error in file(file, "r") : cannot open the connection
Calls: BRGM -> psical -> matrix -> scan -> file
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.7Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/glmmfields.Rcheck/00install.out' for details.
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  21.2Mb
Running examples in 'glmnetUtils-Ex.R' failed
The error most likely occurred in:

> ### Name: cva.glmnet
> ### Title: Do elastic net cross-validation for alpha and lambda
> ###   simultaneously
> ### Aliases: cva.glmnet cva.glmnet.default cva.glmnet.formula
> ###   predict.cva.glmnet predict.cva.glmnet.formula coef.cva.glmnet
> ###   print.cva.glmnet.formula plot.cva.glmnet minlossplot
> ###   minlossplot.cva.glmnet
> 
> ### ** Examples
> 
> cva <- cva.glmnet(mpg ~ ., data=mtcars)
Warning in cbind2(1, newx) :
  number of rows of result is not a multiple of vector length (arg 1)
Error in weighted.mean.default(newX[, i], ...) : 
  'x' and 'w' must have the same length
Calls: cva.glmnet ... do.call -> cv.elnet -> apply -> FUN -> weighted.mean.default
Execution halted
Package suggested but not available for checking: 'cplexAPI'
Running 'test-all.R' [51s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library("testthat")
  > library("GMCM")
  > 
  > test_check("GMCM")
  -- 1. Error: EMAlgorithm returns properly formatted output (@test-EMAlgorithm.R#
  Delta likelihood was negative. Something went wrong!
  1: suppressWarnings({
         res <- GMCM:::EMAlgorithm(dat$z, m = m, max.ite = 100, trace.theta = trace_theta)
     }) at testthat/test-EMAlgorithm.R:12
  2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  3: GMCM:::EMAlgorithm(dat$z, m = m, max.ite = 100, trace.theta = trace_theta) at testthat/test-EMAlgorithm.R:13
  4: stop("Delta likelihood was negative. Something went wrong!") at D:/temp/RtmpANjXVt/R.INSTALL2fbf85cfedb/GMCM/R/EMAlgortihm.R:88
  
  == testthat results  ===========================================================
  OK: 2172 SKIPPED: 2 FAILED: 1
  1. Error: EMAlgorithm returns properly formatted output (@test-EMAlgorithm.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
File 'gnmf/libs/i386/gnmf.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'FactorMatrix.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'FactorMatrix.o'
File 'gnmf/libs/x64/gnmf.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'FactorMatrix.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'FactorMatrix.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Error(s) in re-building vignettes:
--- re-building 'custom_checks.Rmd' using rmarkdown
--- finished re-building 'custom_checks.Rmd'

--- re-building 'goodpractice.Rmd' using rmarkdown
* installing *source* package 'badpackage' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  'badpackage' 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (badpackage)
SUMMARY: processing the following file failed:
  'goodpractice.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    R  27.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/groupedSurv.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'dse1'
Running examples in 'GSE-Ex.R' failed
The error most likely occurred in:

> ### Name: TSGS
> ### Title: Two-Step Generalized S-Estimator for cell- and case-wise
> ###   outliers
> ### Aliases: TSGS
> 
> ### ** Examples
> 
> set.seed(12345)
> 
> # Generate 5% cell-wise contaminated normal data
> # using a random correlation matrix with condition number 100
> x <- generate.cellcontam(n=100, p=10, cond=100, contam.size=5, contam.prop=0.05)
> 
> ## Using MLE
> slrt( cov(x$x), x$A)
[1] 61.72234
> 
> ## Using Fast-S
> slrt( rrcov:::CovSest(x$x)@cov, x$A)
[1] 33.86437
> 
> ## Using 2SGS
> slrt( TSGS(x$x)@S, x$A)
Error: 'DetectDeviatingCells' is not an exported object from 'namespace:cellWise'
Execution halted
Running examples in 'GSE-Ex.R' failed
The error most likely occurred in:

> ### Name: TSGS
> ### Title: Two-Step Generalized S-Estimator for cell- and case-wise
> ###   outliers
> ### Aliases: TSGS
> 
> ### ** Examples
> 
> set.seed(12345)
> 
> # Generate 5% cell-wise contaminated normal data
> # using a random correlation matrix with condition number 100
> x <- generate.cellcontam(n=100, p=10, cond=100, contam.size=5, contam.prop=0.05)
> 
> ## Using MLE
> slrt( cov(x$x), x$A)
[1] 69.01395
> 
> ## Using Fast-S
> slrt( rrcov:::CovSest(x$x)@cov, x$A)
[1] 44.9836
> 
> ## Using 2SGS
> slrt( TSGS(x$x)@S, x$A)
Error: 'DetectDeviatingCells' is not an exported object from 'namespace:cellWise'
Execution halted
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.
Error(s) in re-building vignettes:
--- re-building 'gwqs-vignette.Rmd' using rmarkdown
Welcome to package ztable ver 0.2.0
Quitting from lines 118-128 (gwqs-vignette.Rmd) 
Error: processing vignette 'gwqs-vignette.Rmd' failed with diagnostics:
There are no negative b1 in the bootstrapped models
--- failed re-building 'gwqs-vignette.Rmd'

SUMMARY: processing the following file failed:
  'gwqs-vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/harrietr.Rcheck/00install.out' for details.
Running 'testthat.R' [29s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(harvestr)
  > foreach::registerDoSEQ()
  > test_check("harvestr")
  -- 1. Failure: gather gives the appropriate kinds of seed. (@test-gather.R#42)  
  RNGkind() not identical to c("L'Ecuyer-CMRG", "Inversion").
  Lengths differ: 3 is not 2
  
  -- 2. Failure: gather replaces seed. (@test-gather.R#57)  ----------------------
  RNGkind() not identical to c("Mersenne-Twister", "Box-Muller").
  Lengths differ: 3 is not 2
  
  -- 3. Failure: get.seed retrieves properly (@test-seeds.R#14)  -----------------
  `seed` not identical to `eseed`.
  Mean relative difference: 0.9608917
  
  -- 4. Failure: replace.seed (@test-seeds.R#29)  --------------------------------
  `k` not identical to c("Mersenne-Twister", "Box-Muller").
  Lengths differ: 3 is not 2
  
  -- 5. Failure: replace.seed (@test-seeds.R#30)  --------------------------------
  `l` not identical to c("L'Ecuyer-CMRG", "Inversion").
  Lengths differ: 3 is not 2
  
  -- 6. Failure: withseed replaces previous seed. (@test-seeds.R#56)  ------------
  RNGkind() not identical to c("Mersenne-Twister", "Box-Muller").
  Lengths differ: 3 is not 2
  
  == testthat results  ===========================================================
  OK: 119 SKIPPED: 5 FAILED: 6
  1. Failure: gather gives the appropriate kinds of seed. (@test-gather.R#42) 
  2. Failure: gather replaces seed. (@test-gather.R#57) 
  3. Failure: get.seed retrieves properly (@test-seeds.R#14) 
  4. Failure: replace.seed (@test-seeds.R#29) 
  5. Failure: replace.seed (@test-seeds.R#30) 
  6. Failure: withseed replaces previous seed. (@test-seeds.R#56) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(hdme)
  > 
  > test_check("hdme")
  -- 1. Failure: cv_corrected_lasso computes correctly (@test_corrected_lasso.R#27
  round(cv_fit$loss_min, 2) not equal to round(1.13, 2).
  1/1 mismatches
  [1] 0.98 - 1.13 == -0.15
  
  -- 2. Failure: cv_corrected_lasso computes correctly (@test_corrected_lasso.R#28
  round(cv_fit$radius_1se, 2) not equal to round(1.1, 2).
  1/1 mismatches
  [1] 2.19 - 1.1 == 1.09
  
  -- 3. Failure: cv_corrected_lasso computes correctly (@test_corrected_lasso.R#29
  round(cv_fit$loss_1se, 2) not equal to round(1.52, 2).
  1/1 mismatches
  [1] 0.98 - 1.52 == -0.54
  
  == testthat results  ===========================================================
  OK: 9 SKIPPED: 0 FAILED: 3
  1. Failure: cv_corrected_lasso computes correctly (@test_corrected_lasso.R#27) 
  2. Failure: cv_corrected_lasso computes correctly (@test_corrected_lasso.R#28) 
  3. Failure: cv_corrected_lasso computes correctly (@test_corrected_lasso.R#29) 
  
  Error: testthat unit tests failed
  Execution halted
The following directory looks like a leftover from 'knitr':
  'cache'
Please remove from your package.
Error loading dataset 'dataExample':
   Error in .requirePackage(package) : 
    unable to find required package 'HiTC'
  
  The dataset(s) may use package(s) not declared in the DESCRIPTION file.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc           3.7Mb
    htmlwidgets   4.0Mb
PlotOptPower: no visible global function definition for 'bmp'
PlotOptPower: no visible global function definition for
  'filled.contour'
PlotOptPower: no visible global function definition for 'title'
PlotOptPower: no visible global function definition for 'grey.colors'
PlotOptPower: no visible global function definition for 'axis'
PlotOptPower: no visible global function definition for 'polygon'
PlotOptPower: no visible global function definition for 'legend'
PlotOptPower: no visible global function definition for 'mtext'
PlotOptPower: no visible global function definition for 'dev.off'
PlotOptPower: no visible global function definition for
  'terrain.colors'
ShowOptDesign: no visible global function definition for 'head'
diffVariantError: no visible global function definition for 'pbinom'
predictPoolNCP: no visible global function definition for 'data'
probDetEqual3: no visible global function definition for 'dbinom'
probDetEqual3: no visible global function definition for 'pbinom'
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
See 'd:/Rcompile/CRANpkg/local/3.6/HiResTEC.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.9Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.5Mb
    libs   1.5Mb
File 'hSDM/libs/i386/hSDM.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'useful.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'hSDM.Nmixture.o', 'hSDM.Nmixture.iCAR.o', 'hSDM.ZIB.o',
      'hSDM.ZIB.iCAR.alteration.o', 'hSDM.ZIB.iCAR.o', 'hSDM.ZIP.o',
      'hSDM.ZIP.iCAR.alteration.o', 'hSDM.ZIP.iCAR.o',
      'hSDM.binomial.o', 'hSDM.binomial.iCAR.o', 'hSDM.poisson.o',
      'hSDM.poisson.iCAR.o', 'hSDM.siteocc.o', 'hSDM.siteocc.iCAR.o'
File 'hSDM/libs/x64/hSDM.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'useful.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'hSDM.Nmixture.o', 'hSDM.Nmixture.iCAR.o', 'hSDM.ZIB.o',
      'hSDM.ZIB.iCAR.alteration.o', 'hSDM.ZIB.iCAR.o', 'hSDM.ZIP.o',
      'hSDM.ZIP.iCAR.alteration.o', 'hSDM.ZIP.iCAR.o',
      'hSDM.binomial.o', 'hSDM.binomial.iCAR.o', 'hSDM.poisson.o',
      'hSDM.poisson.iCAR.o', 'hSDM.siteocc.o', 'hSDM.siteocc.iCAR.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data  12.0Mb
    doc    2.2Mb
Running examples in 'hurricaneexposure-Ex.R' failed
The error most likely occurred in:

> ### Name: default_map
> ### Title: Create a default map with eastern US states
> ### Aliases: default_map
> 
> ### ** Examples
> 
> default_map()
Error in loadNamespace(name) : there is no package called 'mapproj'
Calls: <Anonymous> ... mapply -> <Anonymous> -> <Anonymous> -> f -> mproject
Execution halted
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(hutils)
  > 
  > test_check("hutils")
  -- 1. Failure: Mutate other weighted with mass (@test_1-0-0_mutate_other.R#206) 
  uniqueN(routes_pax_othered[["dest"]]) not equal to 7.
  1/1 mismatches
  [1] 6 - 7 == -1
  
  == testthat results  ===========================================================
  OK: 591 SKIPPED: 14 FAILED: 1
  1. Failure: Mutate other weighted with mass (@test_1-0-0_mutate_other.R#206) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(hyphenatr)
  > 
  > test_check("hyphenatr")
  -- 1. Failure: we can do something (@test-hyphenatr.R#16)  ---------------------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "tÃ¤=gelÃ®ch"
  y[1]: "tä=gelîch"
  
  == testthat results  ===========================================================
  OK: 4 SKIPPED: 0 FAILED: 1
  1. Failure: we can do something (@test-hyphenatr.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.1Mb
Running examples in 'IBDsim-Ex.R' failed
The error most likely occurred in:

> ### Name: oneLocusIBD
> ### Title: Estimating pairwise IBD coefficients
> ### Aliases: oneLocusIBD
> ### Keywords: math
> 
> ### ** Examples
> 
> ### Example 1: Full siblings
> x <- nuclearPed(2) 
> Nsim <- 100 # Should be increased substantially
> 
> # Autosomal kappa: Estimate vs exact 
> k_est = oneLocusIBD(x, ind1=3, ind2=4, Nsim=Nsim, seed=123)
---------------
Performing unconditional simulation
Mode: autosomal 
Recombination model: haldane (poisson process) 
Number of simulations: 100 
Simulation finished. Time used: 0.06 seconds
---------------
IBD analysis finished. Total time used: 0.06 seconds.
> k_exact = c(0.25, 0.5, 0.25)
> stopifnot(all(round(k_est - k_exact, 1) == 0))
Error: all(round(k_est - k_exact, 1) == 0) is not TRUE
Execution halted
Running examples in 'IBDsim-Ex.R' failed
The error most likely occurred in:

> ### Name: oneLocusIBD
> ### Title: Estimating pairwise IBD coefficients
> ### Aliases: oneLocusIBD
> ### Keywords: math
> 
> ### ** Examples
> 
> ### Example 1: Full siblings
> x <- nuclearPed(2) 
> Nsim <- 100 # Should be increased substantially
> 
> # Autosomal kappa: Estimate vs exact 
> k_est = oneLocusIBD(x, ind1=3, ind2=4, Nsim=Nsim, seed=123)
---------------
Performing unconditional simulation
Mode: autosomal 
Recombination model: haldane (poisson process) 
Number of simulations: 100 
Simulation finished. Time used: 0.05 seconds
---------------
IBD analysis finished. Total time used: 0.05 seconds.
> k_exact = c(0.25, 0.5, 0.25)
> stopifnot(all(round(k_est - k_exact, 1) == 0))
Error: all(round(k_est - k_exact, 1) == 0) is not TRUE
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
installed size is 23.0Mb
  sub-directories of 1Mb or more:
    R     14.5Mb
    doc    4.8Mb
    libs   2.9Mb
Error(s) in re-building vignettes:
--- re-building 'CMS-HCC.Rmd' using rmarkdown
--- finished re-building 'CMS-HCC.Rmd'

--- re-building 'ICD-10.Rmd' using rmarkdown
--- finished re-building 'ICD-10.Rmd'

--- re-building 'PCCC.Rmd' using rmarkdown
--- finished re-building 'PCCC.Rmd'

--- re-building 'charlson-scores.Rmd' using rmarkdown
--- finished re-building 'charlson-scores.Rmd'

--- re-building 'compare-maps.Rmd' using rmarkdown
--- finished re-building 'compare-maps.Rmd'

--- re-building 'efficiency.Rmd' using rmarkdown
Error: processing vignette 'efficiency.Rmd' failed with diagnostics:
pandoc version 2.2 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
--- failed re-building 'efficiency.Rmd'

--- re-building 'introduction.Rmd' using rmarkdown
--- finished re-building 'introduction.Rmd'

--- re-building 'ranges.Rmd' using rmarkdown
--- finished re-building 'ranges.Rmd'

SUMMARY: processing the following file failed:
  'efficiency.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      1.8Mb
Running examples in 'icsurvROC-Ex.R' failed
The error most likely occurred in:

> ### Name: icsurvROC
> ### Title: Interval Censored survival ROC
> ### Aliases: icsurvROC
> ### Keywords: Semiparametric Cox proportional hazards, local NPMLE, maximum
> ###   likelihood croos validation
> 
> ### ** Examples
> 
> Time=   c(1,2,5,3,9,8,9,4,6,4)
> Status= c(1,1,1,0,1,1,1,0,0,0)
> Marker= c(8,2,6,3,1,4,5,1,3,7)
> 
> #np at year 3
> nobs=length(Time)
> span=sd(Marker)*nobs^(-1/7)
> RES1=icsurvROC(Time, Status, Marker, pred.time=3, method="np", span=span)
> print(RES1)
$tpf
 [1] 1.0000000 0.8264495 0.7402257 0.5663736 0.4751137 0.3892563 0.2863814
 [8] 0.1562429 0.0000000 0.0000000

$fpf
 [1] 1.00000000 0.78620335 0.67901738 0.46537808 0.36081908 0.25344200
 [7] 0.15494160 0.07066247 0.00000000 0.00000000

$cut.value
 [1] -Inf    1    2    3    4    5    6    7    8  Inf

$auc
[1] 0.5770804

$eval.time
[1] 3

> 
> #sp at year 3
> RES2=icsurvROC(Time, Status, Marker, pred.time=3, method="sp")
[1] "Proportional hazards model does not converge"
Error in if (St != 1) tpf.a[i] = (1 - Fc - Sct)/(1 - St) : 
  missing value where TRUE/FALSE needed
Calls: icsurvROC -> icROC
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  13.9Mb
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       5.3Mb
    include   2.8Mb
    libs     12.9Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(incidence)
  > 
  > test_check("incidence")
  -- 1. Failure: construction - numeric input (@test-incidence.R#90)  ------------
  `incidence(dat_num)` produced unexpected warnings.
  Expected match: Flooring from non-integer date caused approximations:\nMean relative difference: 0.0228833
  Actual values:
  * Flooring from non-integer date caused approximations:
  Mean relative difference: 0.02304147
  
  -- 2. Failure: Expected values, no group (@test-incidence.R#312)  --------------
  `res3` has changed from known value recorded in 'rds/incidence.res3.rds'.
  Component "counts": Mean relative difference: 0.3271538
  
  -- 3. Failure: Expected values, no group (@test-incidence.R#313)  --------------
  `res4` has changed from known value recorded in 'rds/incidence.res4.rds'.
  Component "counts": Mean relative difference: 0.9704142
  
  -- 4. Failure: Expected values, no group (@test-incidence.R#316)  --------------
  `res7` has changed from known value recorded in 'rds/incidence.res7.rds'.
  Component "counts": Mean relative difference: 0.172
  
  -- 5. Failure: Expected values, no group (@test-incidence.R#317)  --------------
  `res8` has changed from known value recorded in 'rds/incidence.res8.rds'.
  Component "counts": Mean relative difference: 0.1052632
  
  == testthat results  ===========================================================
  OK: 218 SKIPPED: 18 FAILED: 5
  1. Failure: construction - numeric input (@test-incidence.R#90) 
  2. Failure: Expected values, no group (@test-incidence.R#312) 
  3. Failure: Expected values, no group (@test-incidence.R#313) 
  4. Failure: Expected values, no group (@test-incidence.R#316) 
  5. Failure: Expected values, no group (@test-incidence.R#317) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [15s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(infer)
  > 
  > test_check("infer")
  Setting `type = "permute"` in `generate()`.
  -- 1. Failure: conf_int argument works (@test-wrappers.R#141)  -----------------
  no_var_equal == var_equal isn't false.
  
  -- 2. Failure: conf_int argument works (@test-wrappers.R#153)  -----------------
  shortcut_no_var_equal == shortcut_var_equal isn't false.
  
  == testthat results  ===========================================================
  OK: 347 SKIPPED: 0 FAILED: 2
  1. Failure: conf_int argument works (@test-wrappers.R#141) 
  2. Failure: conf_int argument works (@test-wrappers.R#153) 
  
  Error: testthat unit tests failed
  Execution halted
Missing or unexported object: 'devtools::find_rtools'
ClearBottomMenuPlot: no visible global function definition for 'rect'
InteractiveIGraph : mousedown: no visible global function definition
  for 'grconvertX'
InteractiveIGraph : mousedown: no visible global function definition
  for 'grconvertY'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'grconvertX'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'grconvertY'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'polygon'
InteractiveIGraph : mouseup: no visible global function definition for
  'grconvertX'
InteractiveIGraph : mouseup: no visible global function definition for
  'grconvertY'
InteractiveIGraph : keybd: no visible global function definition for
  'readClipboard'
InteractiveIGraph : keybd: no visible global function definition for
  'par'
PlotRegionGeneral: no visible global function definition for 'polygon'
plot.InteractiveIGraph: no visible global function definition for
  'plot'
plot.InteractiveIGraph: no visible global function definition for 'par'
plot.Menu: no visible global function definition for 'par'
plot.Menu: no visible binding for global variable 'rect'
plot.MenuItem: no visible binding for global variable 'strwidth'
plot.MenuItem: no visible binding for global variable 'strheight'
plot.MenuItem: no visible binding for global variable 'rect'
plot.MenuItem: no visible binding for global variable 'text'
plot.MenuLine: no visible binding for global variable 'rect'
Undefined global functions or variables:
  grconvertX grconvertY par plot polygon readClipboard rect strheight
  strwidth text
Consider adding
  importFrom("graphics", "grconvertX", "grconvertY", "par", "plot",
             "polygon", "rect", "strheight", "strwidth", "text")
  importFrom("utils", "readClipboard")
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.
File 'iotools/libs/i386/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'
File 'iotools/libs/x64/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'

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

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

> ### Name: idstrsplit
> ### Title: Create an iterator for splitting binary or character input into
> ###   a dataframe
> ### Aliases: idstrsplit
> ### Keywords: iterator
> 
> ### ** Examples
> 
> col_names <- names(iris)
> write.csv(iris, file="iris.csv", row.names=FALSE)
> it <- idstrsplit("iris.csv", col_types=c(rep("numeric", 4), "character"), 
+                  sep=",")
> # Get the elements
> iris_read <- it$nextElem()[-1,]
> # or with the iterators package
> # nextElem(it)
> names(iris_read) <- col_names
> print(head(iris_read))
  Sepal.Length Sepal.Width Petal.Length Petal.Width  Species
2          5.1         3.5          1.4         0.2 "setosa"
3          4.9         3.0          1.4         0.2 "setosa"
4          4.7         3.2          1.3         0.2 "setosa"
5          4.6         3.1          1.5         0.2 "setosa"
6          5.0         3.6          1.4         0.2 "setosa"
7          5.4         3.9          1.7         0.4 "setosa"
> unlink("iris.csv")
> 
> 
> 
> cleanEx()
Error: connections left open:
	iris.csv (file)
Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data      1.3Mb
    extdata   7.5Mb
Running examples in 'iRF-Ex.R' failed
The error most likely occurred in:

> ### Name: readForest
> ### Title: Pass data through a fitted forest, record node characteristics
> ###   [works for binary classification with continuous variables]
> ### Aliases: readForest
> 
> ### ** Examples
> 
>   n = 50; p = 10
>   X = array(rnorm(n*p), c(n, p))
>   Y = (X[,1]>0.35 & X[,2]>0.35)|(X[,5]>0.35 & X[,7]>0.35)
>   Y = as.factor(as.numeric(Y>0))
> 
>   train.id = 1:(n/2)
>   test.id = setdiff(1:n, train.id)
>   
>   rf <- randomForest(x=X, y=Y, keep.forest=TRUE, track.nodes=TRUE,
+     ntree=100)
>   rforest <- readForest(rfobj=rf, x=X, n.core=2)
>   head(rforest$tree_info)
NULL
> 
>  # count number of leaf nodes with at least 5 observations
>   sum(rforest$tree.info$size.node > 5)
[1] 293
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11512 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11512 (sockconn)
Execution halted
Running examples in 'iRF-Ex.R' failed
The error most likely occurred in:

> ### Name: readForest
> ### Title: Pass data through a fitted forest, record node characteristics
> ###   [works for binary classification with continuous variables]
> ### Aliases: readForest
> 
> ### ** Examples
> 
>   n = 50; p = 10
>   X = array(rnorm(n*p), c(n, p))
>   Y = (X[,1]>0.35 & X[,2]>0.35)|(X[,5]>0.35 & X[,7]>0.35)
>   Y = as.factor(as.numeric(Y>0))
> 
>   train.id = 1:(n/2)
>   test.id = setdiff(1:n, train.id)
>   
>   rf <- randomForest(x=X, y=Y, keep.forest=TRUE, track.nodes=TRUE,
+     ntree=100)
>   rforest <- readForest(rfobj=rf, x=X, n.core=2)
>   head(rforest$tree_info)
NULL
> 
>  # count number of leaf nodes with at least 5 observations
>   sum(rforest$tree.info$size.node > 5)
[1] 284
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11214 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11214 (sockconn)
Execution halted
Found the following significant warnings:
  Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
See 'd:/Rcompile/CRANpkg/local/3.6/IsoGene.Rcheck/00install.out' for details.
Running examples in 'iterators-Ex.R' failed
The error most likely occurred in:

> ### Name: ireadLines
> ### Title: Iterator over Lines of Text from a Connection
> ### Aliases: ireadLines
> ### Keywords: utilities
> 
> ### ** Examples
> 
>   # create an iterator over the lines of COPYING
>   it <- ireadLines(file.path(R.home(), 'COPYING'))
>   nextElem(it)
[1] "\t\t    GNU GENERAL PUBLIC LICENSE"
>   nextElem(it)
[1] "\t\t       Version 2, June 1991"
>   nextElem(it)
[1] ""
> 
> 
> 
> cleanEx()
Error: connections left open:
	D:/RCompile/recent/R/COPYING (file)
Execution halted
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(janitor)
  > 
  > test_check("janitor")
  -- 1. Failure: users can supply own Ns (@test-adorn-ns.R#129)  -----------------
  `%>%`(...) not equal to data.frame(...).
  Component "big": 2 string mismatches
  Component "small": 2 string mismatches
  
  == testthat results  ===========================================================
  OK: 438 SKIPPED: 0 FAILED: 1
  1. Failure: users can supply own Ns (@test-adorn-ns.R#129) 
  
  Error: testthat unit tests failed
  Execution halted
Package unavailable to check Rd xrefs: 'doMC'
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    dict  19.2Mb
Running 'testthat.R' [33s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(jpmesh)
  > 
  > test_check("jpmesh")
  -- 1. Failure: Generate random meshcode (@test-rmesh.R#8)  ---------------------
  `res` not equal to "50304610".
  1/1 mismatches
  x[1]: "64394175"
  y[1]: "50304610"
  
  == testthat results  ===========================================================
  OK: 133 SKIPPED: 0 FAILED: 1
  1. Failure: Generate random meshcode (@test-rmesh.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(kamila)
  > 
  > test_check("kamila")
  -- 1. Failure: gmsClust runs as expected, small data set (@test_gmsClust.R#13)  
  res1$results$cluster not equal to c(1, 1, 2, 1, 1, 2, 1, 2, 2, 1, 2, 1, 2, 2, 2).
  6/15 mismatches (average diff: 1)
  [1]  2 - 1 ==  1
  [3]  1 - 2 == -1
  [6]  1 - 2 == -1
  [8]  1 - 2 == -1
  [11] 1 - 2 == -1
  [15] 1 - 2 == -1
  
  -- 2. Failure: KAMILA runs as expected, small data set (@test_kamila.R#19)  ----
  res1$finalMemb not identical to c(2, 1, 2, 1, 1, 2, 1, 1, 1, 2, 1, 1, 2, 2, 1).
  15/15 mismatches (average diff: 1)
  [1] 1 - 2 == -1
  [2] 2 - 1 ==  1
  [3] 1 - 2 == -1
  [4] 2 - 1 ==  1
  [5] 2 - 1 ==  1
  [6] 1 - 2 == -1
  [7] 2 - 1 ==  1
  [8] 2 - 1 ==  1
  [9] 2 - 1 ==  1
  ...
  
  == testthat results  ===========================================================
  OK: 2 SKIPPED: 0 FAILED: 2
  1. Failure: gmsClust runs as expected, small data set (@test_gmsClust.R#13) 
  2. Failure: KAMILA runs as expected, small data set (@test_kamila.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
See 'd:/Rcompile/CRANpkg/local/3.6/KANT.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
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.
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(kmer)
  > test_check("kmer")
  Converting to Dayhoff(6) compressed alphabet for k > 4
  Classes: AGPST, C, DENQ, FWY, HKR, ILMV-- 1. Failure: object dimensions are correct (@test_distance.R#103)  -----------
  ncol(y.mbed) not equal to 9.
  1/1 mismatches
  [1] 8 - 9 == -1
  
  == testthat results  ===========================================================
  OK: 24 SKIPPED: 0 FAILED: 1
  1. Failure: object dimensions are correct (@test_distance.R#103) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(kmer)
  > test_check("kmer")
  Converting to Dayhoff(6) compressed alphabet for k > 4
  Classes: AGPST, C, DENQ, FWY, HKR, ILMV-- 1. Failure: object dimensions are correct (@test_distance.R#103)  -----------
  ncol(y.mbed) not equal to 9.
  1/1 mismatches
  [1] 8 - 9 == -1
  
  == testthat results  ===========================================================
  OK: 24 SKIPPED: 0 FAILED: 1
  1. Failure: object dimensions are correct (@test_distance.R#103) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   6.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.1Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:72:36: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:96:9: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.6/LANDD.Rcheck/00install.out' for details.
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Running examples in 'LCA-Ex.R' failed
The error most likely occurred in:

> ### Name: LCA
> ### Title: Localised Co-dependency Analysis
> ### Aliases: LCA
> 
> ### ** Examples
> 
> ## create a data matrix
> 
> x <- array(runif(1200),dim=c(40,12))
> 
> ## implant similarity across a 'clique'
> 
> clique.cols <- sample(ncol(x),4)
> x[,clique.cols] <- x[,clique.cols] + rnorm(nrow(x))
> 
> ## scale x to (0,1)
> 
> x[x<0] <- 0
> x[x>1] <- 1
> 
> ## choose a 'seed' feature and some partner
> 
> seed.row <- sample(nrow(x),1)
> partner.row <- sample(setdiff(c(1:nrow(x)),seed.row),1)
> 
> x[c(seed.row,partner.row),clique.cols] <- x[c(seed.row,partner.row),clique.cols] + 
+ rep(rnorm(length(clique.cols)),each=2)
> 
> ## calibrate PTL models to dataset
> 
> PTL.fit <- fitPTLmodel(x,nPairs=15)
1 models successfully fitted out of 12 
Error in fitPTLmodel(x, nPairs = 15) : 
  Rerun model calibration (possibly with higher nPairs), no successful fits this time.
Execution halted
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
Running examples in 'liayson-Ex.R' failed
The error most likely occurred in:

> ### Name: clusterCells
> ### Title: Grouping cells into clones.
> ### Aliases: clusterCells
> 
> ### ** Examples
> 
> data(cnps)
> set.seed(2)
> rcells = sample(colnames(cnps), 120)
> outc = clusterCells(cnps[apply(cnps, 1, var)>0, rcells])
[1] "Neither k nor h is set."
[1] "Using Akaike information criterion to decide number of clusters..."
Error in kmeans(t(cnps), centers = x) : 
  more cluster centers than distinct data points.
Calls: clusterCells ... sapply -> lapply -> FUN -> .kmeansAIC -> ncol -> kmeans
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   2.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
    libs   1.5Mb
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("lineup")
  Loading required package: lineup
  -- 1. Failure: corbetw2mat works in the other cases (@test-corbetw2mat.R#45)  --
  `result1` not equal to `expected1`.
  Component "yindex": Mean relative difference: 0.3125
  Component "ycol": Attributes: < Component "levels": 2 string mismatches >
  Component "ycol": 3 string mismatches
  
  -- 2. Failure: corbetw2mat works in the other cases (@test-corbetw2mat.R#55)  --
  `result2` not equal to `expected2`.
  Component "cor": Mean relative difference: 0.3670566
  Component "yindex": Mean relative difference: 0.2083333
  Component "ycol": Attributes: < Component "levels": 4 string mismatches >
  Component "ycol": 4 string mismatches
  
  == testthat results  ===========================================================
  OK: 3 SKIPPED: 0 FAILED: 2
  1. Failure: corbetw2mat works in the other cases (@test-corbetw2mat.R#45) 
  2. Failure: corbetw2mat works in the other cases (@test-corbetw2mat.R#55) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("lineup")
  Loading required package: lineup
  -- 1. Failure: corbetw2mat works in the other cases (@test-corbetw2mat.R#45)  --
  `result1` not equal to `expected1`.
  Component "yindex": Mean relative difference: 0.3125
  Component "ycol": Attributes: < Component "levels": 2 string mismatches >
  Component "ycol": 3 string mismatches
  
  -- 2. Failure: corbetw2mat works in the other cases (@test-corbetw2mat.R#55)  --
  `result2` not equal to `expected2`.
  Component "cor": Mean relative difference: 0.8494099
  Component "yindex": Mean relative difference: 0.2083333
  Component "ycol": Attributes: < Component "levels": 4 string mismatches >
  Component "ycol": 4 string mismatches
  
  == testthat results  ===========================================================
  OK: 3 SKIPPED: 0 FAILED: 2
  1. Failure: corbetw2mat works in the other cases (@test-corbetw2mat.R#45) 
  2. Failure: corbetw2mat works in the other cases (@test-corbetw2mat.R#55) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
See 'd:/Rcompile/CRANpkg/local/3.6/LipidMS.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.0Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs       2.1Mb
    testdata   1.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(lolR)
  > 
  > test_check("lolR")
  -- 1. Failure: Optimal Embedding Dimensions (@test-xval.R#45)  -----------------
  result.rs$optimal.lhat not equal to result.rs.noset$optimal.lhat.
  Lengths differ: 2 is not 1
  
  == testthat results  ===========================================================
  OK: 446 SKIPPED: 0 FAILED: 1
  1. Failure: Optimal Embedding Dimensions (@test-xval.R#45) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [38s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(loo)
  This is loo version 2.0.0.
  **NOTE: As of version 2.0.0 loo defaults to 1 core but we recommend using as many as possible. Use the 'cores' argument or set options(mc.cores = NUM_CORES) for an entire session. Visit mc-stan.org/loo/news for details on other changes.
  
  Attaching package: 'loo'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  > Sys.setenv("R_TESTS" = "")
  > test_check("loo")
  -- 1. Failure: weighted quantiles work (@test_E_loo.R#155)  --------------------
  .wquant(x1, w1, pr) not equal to .wquant_sim(x1, w1, pr, n_sim = 2e+06).
  35/39 mismatches (average diff: 0.012)
  [1]  -2.005 - -1.987 == -0.01808
  [2]  -1.688 - -1.647 == -0.04073
  [3]  -1.472 - -1.440 == -0.03245
  [4]  -1.269 - -1.280 ==  0.01101
  [5]  -1.143 - -1.152 ==  0.00863
  [6]  -1.040 - -1.042 ==  0.00202
  [7]  -0.946 - -0.943 == -0.00287
  [8]  -0.831 - -0.837 ==  0.00630
  [10] -0.658 - -0.667 ==  0.00869
  ...
  
  == testthat results  ===========================================================
  OK: 378 SKIPPED: 0 FAILED: 1
  1. Failure: weighted quantiles work (@test_E_loo.R#155) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      1.5Mb
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(lsbclust)
  Loading required package: ggplot2
  > 
  > test_check("lsbclust")
  K-means on overall means...	DONE
  -- 1. Failure: cluster vector (@test_orc.R#29)  --------------------------------
  ovl$cluster not identical to ovltest$cluster.
  24/220 mismatches (average diff: 1.33)
  [1]    8 - 10 == -2
  [14]  10 -  9 ==  1
  [31]   9 -  8 ==  1
  [57]   9 -  8 ==  1
  [61]   8 - 10 == -2
  [64]   8 - 10 == -2
  [77]  10 -  9 ==  1
  [84]  10 -  9 ==  1
  [112]  9 -  8 ==  1
  ...
  
  -- 2. Failure: cluster means (@test_orc.R#33)  ---------------------------------
  ovl$centers not equal to ovltest$centers.
  3/12 mismatches (average diff: 3.68)
  [8]  7.22 - 2.70 ==  4.52
  [9]  2.70 - 1.70 ==  1.00
  [10] 1.70 - 7.22 == -5.52
  
  K-means on row margins...	DONE
  K-means on column margins...	DONE
  == testthat results  ===========================================================
  OK: 34 SKIPPED: 0 FAILED: 2
  1. Failure: cluster vector (@test_orc.R#29) 
  2. Failure: cluster means (@test_orc.R#33) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(lsbclust)
  Loading required package: ggplot2
  > 
  > test_check("lsbclust")
  K-means on overall means...	DONE
  -- 1. Failure: cluster vector (@test_orc.R#29)  --------------------------------
  ovl$cluster not identical to ovltest$cluster.
  24/220 mismatches (average diff: 1.33)
  [1]    8 - 10 == -2
  [14]  10 -  9 ==  1
  [31]   9 -  8 ==  1
  [57]   9 -  8 ==  1
  [61]   8 - 10 == -2
  [64]   8 - 10 == -2
  [77]  10 -  9 ==  1
  [84]  10 -  9 ==  1
  [112]  9 -  8 ==  1
  ...
  
  -- 2. Failure: cluster means (@test_orc.R#33)  ---------------------------------
  ovl$centers not equal to ovltest$centers.
  3/12 mismatches (average diff: 3.68)
  [8]  7.22 - 2.70 ==  4.52
  [9]  2.70 - 1.70 ==  1.00
  [10] 1.70 - 7.22 == -5.52
  
  K-means on row margins...	DONE
  K-means on column margins...	DONE
  == testthat results  ===========================================================
  OK: 34 SKIPPED: 0 FAILED: 2
  1. Failure: cluster vector (@test_orc.R#29) 
  2. Failure: cluster means (@test_orc.R#33) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(lucr)
  > 
  > test_check("lucr")
  -- 1. Failure: Simple amounts can be converted (@test_conversion.R#4)  ---------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "Â£12.00"
  y[1]: "£12.00"
  
  -- 2. Failure: Complex amounts can be converted (@test_conversion.R#8)  --------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "Â£12,000.00"
  y[1]: "£12,000.00"
  
  == testthat results  ===========================================================
  OK: 6 SKIPPED: 0 FAILED: 2
  1. Failure: Simple amounts can be converted (@test_conversion.R#4) 
  2. Failure: Complex amounts can be converted (@test_conversion.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   1.6Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
    proj   5.0Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    TS_files     5.8Mb
    base_files   6.3Mb
installed size is 41.3Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs  34.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc           1.2Mb
    htmlwidgets   1.4Mb
    libs          7.6Mb
Running examples in 'markmyassignment-Ex.R' failed
The error most likely occurred in:

> ### Name: mark_my_file
> ### Title: Mark assignment file
> ### Aliases: mark_my_file
> 
> ### ** Examples
> 
> assignment_path <- 
+   paste0(system.file(package = "markmyassignment"), "/extdata/example_assignment01.yml")
> file_path <- paste0(system.file(package = "markmyassignment"), "/extdata/example_lab_file.R")
> mark_my_file(mark_file = file_path, assignment_path = assignment_path)
v | OK F W S | Context

/ |  0       | task1
- |  1       | task1
\ |  2       | task1
| |  3       | task1
v |  3       | task1

/ |  0       | task2a
- |  1       | task2a
\ |  2       | task2a
| |  3       | task2a
v |  3       | task2a

/ |  0       | task2b
- |  1       | task2b
\ |  2       | task2b
| |  3       | task2b
/ |  4       | task2b
v |  4       | task2b

/ |  0       | Mandatory tests
- |  1       | Mandatory tests
v |  1       | Mandatory tests

== Results =====================================================================
OK:       11
Failed:   0
Warnings: 0
Skipped:  0
Keep up the good work!> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	lines (textConnection)
Execution halted
Error(s) in re-building vignettes:
--- re-building 'GSoC-2017_additions.Rmd' using rmarkdown
Package:  markovchain
Version:  0.6.9.14
Date:     2019-01-20
BugReport: http://github.com/spedygiorgio/markovchain/issues

--- finished re-building 'GSoC-2017_additions.Rmd'

--- re-building 'an_introduction_to_markovchain_package.Rmd' using rmarkdown
Error: processing vignette 'an_introduction_to_markovchain_package.Rmd' failed with diagnostics:
pandoc version 2.2 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
--- failed re-building 'an_introduction_to_markovchain_package.Rmd'

--- re-building 'complicateSteadyStates.Rmd' using rmarkdown
Package:  markovchain
Version:  0.6.9.14
Date:     2019-01-20
BugReport: http://github.com/spedygiorgio/markovchain/issues

--- finished re-building 'complicateSteadyStates.Rmd'

--- re-building 'higher_order_markov_chains.Rmd' using rmarkdown
Error: processing vignette 'higher_order_markov_chains.Rmd' failed with diagnostics:
pandoc version 2.2 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
--- failed re-building 'higher_order_markov_chains.Rmd'

--- re-building 'markovchainCrashIntro.Rmd' using rmarkdown
--- finished re-building 'markovchainCrashIntro.Rmd'

SUMMARY: processing the following files failed:
  'an_introduction_to_markovchain_package.Rmd'
  'higher_order_markov_chains.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   2.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Running 'testthat.R' [20s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(matrixTests)
  > 
  > test_check("matrixTests")
  -- 1. Failure: monte-carlo random testing gives equal results (@test-correct-cor
  `t1` not equal to `t2`.
  Component "conf.level": Mean absolute difference: 0.2742743
  
  == testthat results  ===========================================================
  OK: 836 SKIPPED: 0 FAILED: 1
  1. Failure: monte-carlo random testing gives equal results (@test-correct-cor_pearson.R#58) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   1.6Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.2Mb
Depends: includes the non-default packages:
  'MASS', 'boot', 'RColorBrewer', 'scatterplot3d', 'tcltk', 'tcltk2',
  'tkrplot', 'rpanel', 'rgl'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      1.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.0Mb
Error(s) in re-building vignettes:
--- re-building 'metaBMA.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.
INFORMATION: Es konnten keine Dateien mit dem angegebenen
Muster gefunden werden.
Quitting from lines 63-72 (metaBMA.Rmd) 
Error: processing vignette 'metaBMA.Rmd' failed with diagnostics:
Unable to call JAGS
--- failed re-building 'metaBMA.Rmd'

SUMMARY: processing the following file failed:
  'metaBMA.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Running examples in 'metacart-Ex.R' failed
The error most likely occurred in:

> ### Name: FEmrt
> ### Title: Fixed effect meta-tree
> ### Aliases: FEmrt
> 
> ### ** Examples
> 
> data(dat.BCT2009)
> FEtree <- FEmrt(g ~ T1 + T2+ T4 + T25, vi = vi, data = dat.BCT2009, c = 0.5)
Warning in FEmrt(g ~ T1 + T2 + T4 + T25, vi = vi, data = dat.BCT2009, c = 0.5) :
  no moderator effect was detected
> print(FEtree)

Fixed Effects Meta-Tree (K = 106 studies); 
FEmrt(formula = g ~ T1 + T2 + T4 + T25, data = dat.BCT2009, vi = vi, 
    c = 0.5)

No moderator effect was detected
use summary() to see the meta-analysis results> summary(FEtree)

Fixed Effects meta-tree (K = 106 studies); 
FEmrt(formula = g ~ T1 + T2 + T4 + T25, data = dat.BCT2009, vi = vi, 
    c = 0.5)

No moderator effect was detected

Test for Heterogeneity under FE assumption:
Q = 253.0357 (df = 105), p-value < 1e-04;

Fixed Effect Meta-analysis Results:
   no.      g     se   zval   pval  ci.lb  ci.ub        
   106  0.229  0.012 18.803  0.000  0.206  0.253    *** 
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

> plot(FEtree)
Error in `rownames<-`(`*tmp*`, value = rank(as.numeric(rownames(frame)))) : 
  attempt to set 'rownames' on an object with no dimensions
Calls: plot -> plot.FEmrt -> rownames<-
Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
Packages suggested but not available for checking: 'doMC', 'doSMP'
Running 'testthat.R' [50s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(metR)
  > library(vdiffr)
  > 
  > test_check("metR")
  -- 1. Failure: EOF changes probs (@test_eof.R#21)  -----------------------------
  {
      ...
  } not identical to 1524903.
  1/1 mismatches
  [1] 1523828 - 1524903 == -1075
  
  == testthat results  ===========================================================
  OK: 62 SKIPPED: 16 FAILED: 1
  1. Failure: EOF changes probs (@test_eof.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.1Mb
    libs   4.4Mb
    misc   1.1Mb
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(mgsub)
  > 
  > test_check("mgsub")
  -- 1. Failure: multicharacter censor works (@test_mgsub_censor.R#53)  ----------
  mgsub_censor("What the flip?", "flip", "?#!*", seed = 10) not equal to "What the !##!?".
  1/1 mismatches
  x[1]: "What the !?#*?"
  y[1]: "What the !##!?"
  
  -- 2. Failure: multicharacter censor works (@test_mgsub_censor.R#54)  ----------
  mgsub_censor(...) not equal to "What the !##!?".
  1/1 mismatches
  x[1]: "What the !?#*?"
  y[1]: "What the !##!?"
  
  -- 3. Failure: multicharacter censor works (@test_mgsub_censor.R#55)  ----------
  mgsub_censor("What the flip?", "flip", c("?#", "!*"), seed = 10) not equal to "What the !##!?".
  1/1 mismatches
  x[1]: "What the !?#*?"
  y[1]: "What the !##!?"
  
  -- 4. Failure: multicharacter censor can be used badly (@test_mgsub_censor.R#61)
  mgsub_censor(...) not equal to "What the !*?#?#!*?".
  1/1 mismatches
  x[1]: "What the ?#?#!*!*?"
  y[1]: "What the !*?#?#!*?"
  
  == testthat results  ===========================================================
  OK: 56 SKIPPED: 0 FAILED: 4
  1. Failure: multicharacter censor works (@test_mgsub_censor.R#53) 
  2. Failure: multicharacter censor works (@test_mgsub_censor.R#54) 
  3. Failure: multicharacter censor works (@test_mgsub_censor.R#55) 
  4. Failure: multicharacter censor can be used badly (@test_mgsub_censor.R#61) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [90s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(mice)
  Loading required package: lattice
  
  Attaching package: 'mice'
  
  The following objects are masked from 'package:base':
  
      cbind, rbind
  
  > 
  > test_check("mice")
  -- 1. Failure: retains same numerical result (@test-pool.R#13)  ----------------
  unname(getqbar(est)) not equal to `mn`.
  5/5 mismatches (average diff: 0.895)
  [1] 19.7878 - 18.7617 ==  1.02603
  [2]  0.0513 -  0.0536 == -0.00229
  [3] -6.1563 - -4.5737 == -1.58260
  [4] -7.7136 - -6.6360 == -1.07766
  [5]  2.9521 -  2.1636 ==  0.78847
  
  -- 2. Failure: retains same numerical result (@test-pool.R#14)  ----------------
  unname(summary(est)[, "std.error"]) not equal to `se`.
  5/5 mismatches (average diff: 0.329)
  [1] 3.4259 - 4.0028 == -0.57694
  [2] 0.0187 - 0.0224 == -0.00363
  [3] 1.6195 - 2.0340 == -0.41452
  [4] 1.9746 - 2.4598 == -0.48513
  [5] 1.8642 - 2.0290 == -0.16475
  
  == testthat results  ===========================================================
  OK: 274 SKIPPED: 0 FAILED: 2
  1. Failure: retains same numerical result (@test-pool.R#13) 
  2. Failure: retains same numerical result (@test-pool.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [100s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(mice)
  Loading required package: lattice
  
  Attaching package: 'mice'
  
  The following objects are masked from 'package:base':
  
      cbind, rbind
  
  > 
  > test_check("mice")
  -- 1. Failure: retains same numerical result (@test-pool.R#13)  ----------------
  unname(getqbar(est)) not equal to `mn`.
  5/5 mismatches (average diff: 0.895)
  [1] 19.7878 - 18.7617 ==  1.02603
  [2]  0.0513 -  0.0536 == -0.00229
  [3] -6.1563 - -4.5737 == -1.58260
  [4] -7.7136 - -6.6360 == -1.07766
  [5]  2.9521 -  2.1636 ==  0.78847
  
  -- 2. Failure: retains same numerical result (@test-pool.R#14)  ----------------
  unname(summary(est)[, "std.error"]) not equal to `se`.
  5/5 mismatches (average diff: 0.329)
  [1] 3.4259 - 4.0028 == -0.57694
  [2] 0.0187 - 0.0224 == -0.00363
  [3] 1.6195 - 2.0340 == -0.41452
  [4] 1.9746 - 2.4598 == -0.48513
  [5] 1.8642 - 2.0290 == -0.16475
  
  == testthat results  ===========================================================
  OK: 274 SKIPPED: 0 FAILED: 2
  1. Failure: retains same numerical result (@test-pool.R#13) 
  2. Failure: retains same numerical result (@test-pool.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [24s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > #library(microsamplingDesign)
  > 
  > #source("generateTestData.R")
  > 
  > #test_check("microsamplingDesign")
  > 
  > testthat::test_check("microsamplingDesign")
  Loading required package: microsamplingDesign
  start Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 cores-- 1. Failure: Equal ranking timePoints (@testRankTimePoints.R#43)  ------------
  rankTimePointsOrig@ranking not equal to rankedTimePointsNew@ranking.
  Component "name": 7 string mismatches
  Component "criterion": Mean relative difference: 0.04047401
  
  == testthat results  ===========================================================
  OK: 20 SKIPPED: 4 FAILED: 1
  1. Failure: Equal ranking timePoints (@testRankTimePoints.R#43) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [28s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > #library(microsamplingDesign)
  > 
  > #source("generateTestData.R")
  > 
  > #test_check("microsamplingDesign")
  > 
  > testthat::test_check("microsamplingDesign")
  Loading required package: microsamplingDesign
  start Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 cores-- 1. Failure: Equal ranking timePoints (@testRankTimePoints.R#43)  ------------
  rankTimePointsOrig@ranking not equal to rankedTimePointsNew@ranking.
  Component "name": 7 string mismatches
  Component "criterion": Mean relative difference: 0.04047401
  
  == testthat results  ===========================================================
  OK: 20 SKIPPED: 4 FAILED: 1
  1. Failure: Equal ranking timePoints (@testRankTimePoints.R#43) 
  
  Error: testthat unit tests failed
  Execution halted
File 'MigClim/libs/i386/MigClim.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'genclust.o', 'migrate.o', 'src_cell.o', 'validate.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'genclust.o', 'migrate.o'
File 'MigClim/libs/x64/MigClim.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'genclust.o', 'migrate.o', 'src_cell.o', 'validate.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'genclust.o', 'migrate.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
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.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:72:36: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:96:9: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.6/mixedMem.Rcheck/00install.out' for details.
Package unavailable to check Rd xrefs: 'REBayes'
Running examples in 'ML.MSBD-Ex.R' failed
The error most likely occurred in:

> ### Name: likelihood_MSBD_unresolved
> ### Title: Likelihood calculation for unresolved trees
> ### Aliases: likelihood_MSBD_unresolved
> 
> ### ** Examples
> 
> # Simulate a random phylogeny
> set.seed(24)
> tree <- ape::rcoal(10)
> 
> # Calculate the log likelihood under a constant birth-death model (i.e, no shifts) 
> # with unresolved tips
> likelihood_MSBD_unresolved(tree, shifts = c(), gamma = 0, lambdas = 10, mus = 1, 
+                            lineage_counts = c(2,5,1,3,1,1,1,1,2,6), tcut = 0.05)
Error in likelihood_MSBD_unresolved(tree, shifts = c(), gamma = 0, lambdas = 10,  : 
  Invalid cut-off time for tip t7
Execution halted
Error(s) in re-building vignettes:
--- re-building 'Using_ML.MSBD.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 57-58 (Using_ML.MSBD.Rmd) 
Error: processing vignette 'Using_ML.MSBD.Rmd' failed with diagnostics:
Tree edge 2 has negative length
--- failed re-building 'Using_ML.MSBD.Rmd'

SUMMARY: processing the following file failed:
  'Using_ML.MSBD.Rmd'

Error: Vignette re-building failed.
Execution halted
listGenoToTable: no visible binding for global variable 'dummy'
Undefined global functions or variables:
  dummy
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    1.8Mb
    libs   1.9Mb
Running 'testthat.R' [374s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > # Sys.setenv("MONETDBLITE_INMEMORY" = "yes")
  > # test_check("MonetDBLite")
  > Sys.setenv("MONETDBLITE_INMEMORY" = "no")
  > test_check("MonetDBLite")
  Loading required package: MonetDBLite
  -- 1. Failure: db allows svyby commands (@test_05_survey.R#60)  ----------------
  round(...) not equal to 0.022.
  1/1 mismatches
  [1] 0.019 - 0.022 == -0.003
  
  -- 2. Failure: db allows svyby commands (@test_05_survey.R#62)  ----------------
  ...[] not equal to 10.11.
  1/1 mismatches
  [1] 10.3 - 10.1 == 0.23
  
  [1] "E"
  [1] "H"
  [1] "M"
  -- 3. Failure: db allows svyby commands (@test_05_survey.R#66)  ----------------
  round(SE(a)[2], 2) not equal to 4708.41.
  1/1 mismatches
  [1] 5476 - 4708 == 768
  
  -- 4. Failure: db allows svyby commands (@test_05_survey.R#67)  ----------------
  as.numeric(round(cv(a)[2], 4)) not equal to 0.2975.
  1/1 mismatches
  [1] 0.346 - 0.297 == 0.0486
  
  -- 5. Failure: db allows svyby commands (@test_05_survey.R#69)  ----------------
  round(confint(a, df = degf(rclus1))[2, 2], 2) not equal to 30808.26.
  1/1 mismatches
  [1] 33252 - 30808 == 2443
  
  == testthat results  ===========================================================
  OK: 296 SKIPPED: 13 FAILED: 5
  1. Failure: db allows svyby commands (@test_05_survey.R#60) 
  2. Failure: db allows svyby commands (@test_05_survey.R#62) 
  3. Failure: db allows svyby commands (@test_05_survey.R#66) 
  4. Failure: db allows svyby commands (@test_05_survey.R#67) 
  5. Failure: db allows svyby commands (@test_05_survey.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [256s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > # Sys.setenv("MONETDBLITE_INMEMORY" = "yes")
  > # test_check("MonetDBLite")
  > Sys.setenv("MONETDBLITE_INMEMORY" = "no")
  > test_check("MonetDBLite")
  Loading required package: MonetDBLite
  -- 1. Failure: db allows svyby commands (@test_05_survey.R#60)  ----------------
  round(...) not equal to 0.022.
  1/1 mismatches
  [1] 0.019 - 0.022 == -0.003
  
  -- 2. Failure: db allows svyby commands (@test_05_survey.R#62)  ----------------
  ...[] not equal to 10.11.
  1/1 mismatches
  [1] 10.3 - 10.1 == 0.23
  
  [1] "E"
  [1] "H"
  [1] "M"
  -- 3. Failure: db allows svyby commands (@test_05_survey.R#66)  ----------------
  round(SE(a)[2], 2) not equal to 4708.41.
  1/1 mismatches
  [1] 5476 - 4708 == 768
  
  -- 4. Failure: db allows svyby commands (@test_05_survey.R#67)  ----------------
  as.numeric(round(cv(a)[2], 4)) not equal to 0.2975.
  1/1 mismatches
  [1] 0.346 - 0.297 == 0.0486
  
  -- 5. Failure: db allows svyby commands (@test_05_survey.R#69)  ----------------
  round(confint(a, df = degf(rclus1))[2, 2], 2) not equal to 30808.26.
  1/1 mismatches
  [1] 33252 - 30808 == 2443
  
  == testthat results  ===========================================================
  OK: 296 SKIPPED: 16 FAILED: 5
  1. Failure: db allows svyby commands (@test_05_survey.R#60) 
  2. Failure: db allows svyby commands (@test_05_survey.R#62) 
  3. Failure: db allows svyby commands (@test_05_survey.R#66) 
  4. Failure: db allows svyby commands (@test_05_survey.R#67) 
  5. Failure: db allows svyby commands (@test_05_survey.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
Error(s) in re-building vignettes:
--- re-building 'estimatingWindSpeed.Rmd' using rmarkdown
--- finished re-building 'estimatingWindSpeed.Rmd'

--- re-building 'windEstimationParameters.Rmd' using rmarkdown
Quitting from lines 92-93 (windEstimationParameters.Rmd) 
Error: processing vignette 'windEstimationParameters.Rmd' failed with diagnostics:
some 'x' not counted; maybe 'breaks' do not span range of 'x'
--- failed re-building 'windEstimationParameters.Rmd'

SUMMARY: processing the following file failed:
  'windEstimationParameters.Rmd'

Error: Vignette re-building failed.
Execution halted
Running examples in 'mptools-Ex.R' failed
The error most likely occurred in:

> ### Name: kch
> ### Title: Extract Metapop KCH
> ### Aliases: kch
> 
> ### ** Examples
> 
> mp <- system.file('example.mp', package='mptools')
> k <- kch(meta=meta(mp), path=dirname(mp))
Extracting population metadata from file:
D:/temp/RtmpcNWtQ5/RLIBS_1c19c64b055ed/mptools/example.mp
> 
> 
> 
> cleanEx()
Error: connections left open:
	pops[1] (textConnection)
Execution halted
File 'MRwarping/libs/i386/MRwarping.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'interfaceRC_warp.o'
File 'MRwarping/libs/x64/MRwarping.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'interfaceRC_warp.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
See 'd:/Rcompile/CRANpkg/local/3.6/MSeasy.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
See 'd:/Rcompile/CRANpkg/local/3.6/MSeasyTkGUI.Rcheck/00install.out' for details.
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  19.8Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Running examples in 'msgpack-Ex.R' failed
The error most likely occurred in:

> ### Name: msgConnection
> ### Title: Read and write msgpack formatted messages over R connections.
> ### Aliases: msgConnection close.msgConnection partial
> ###   partial.msgConnection readMsgs status status.msgConnection
> ###   seek.msgConnection readMsg writeMsg writeMsgs
> 
> ### ** Examples
> 
> out <- rawConnection(raw(0), open="wb")
> apply(quakes, 1, function(x) writeMsg(x, out))
NULL
> length(rawConnectionValue(out))
[1] 57300
> inn <- msgConnection(rawConnection(rawConnectionValue(out), open="rb"))
> readMsg(inn)
     lat     long    depth      mag stations 
  -20.42   181.62   562.00     4.80    41.00 
> readMsgs(inn, 3)
[[1]]
     lat     long    depth      mag stations 
  -20.62   181.03   650.00     4.20    15.00 

[[2]]
     lat     long    depth      mag stations 
   -26.0    184.1     42.0      5.4     43.0 

[[3]]
     lat     long    depth      mag stations 
  -17.97   181.66   626.00     4.10    19.00 

> 
> 
> 
> cleanEx()
Error: connections left open:
	raw(0) (rawConnection)
	rawConnectionValue(out) (rawConnection)
Execution halted
Found the following significant warnings:
  Warning: unable to re-encode 'dfgps.R' line 51
  Warning: unable to re-encode 'msgps.R' line 98
  Warning: unable to re-encode 'plot.msgps.R' line 60
  Warning: unable to re-encode 'print.msgps.R' line 36
  Warning: unable to re-encode 'summary.msgps.R' line 45
See 'd:/Rcompile/CRANpkg/local/3.6/msgps.Rcheck/00install.out' for details.
Running 'test_base.R' [46s]
Running the tests in 'tests/test_base.R' failed.
Complete output:
  > library(testthat)
  > test_check("msm")
  Loading required package: msm
  -- 1. Failure: Information matrix (@test_deriv.r#138)  -------------------------
  c(0.88475550512612, 0.202501688704573, -0.474183198550202) not equal to tm$paramdata$info[1:3].
  3/3 mismatches (average diff: 0.284)
  [1]  0.885 -  1.0455 == -0.161
  [2]  0.203 -  0.0872 ==  0.115
  [3] -0.474 - -1.0490 ==  0.575
  
  -- 2. Failure: piecewise constant intensities with pci, with other covariates (@
  448.1228 not equal to cav5cov.msm$minus2loglik.
  1/1 mismatches
  [1] 448 - 456 == -7.79
  
  -- 3. Failure: piecewise constant intensities with pci, with other covariates (@
  448.1228 not equal to cav5cov.msm$minus2loglik.
  1/1 mismatches
  [1] 448 - 456 == -7.79
  
  -- 4. Failure: piecewise constant intensities with pci, with uncentered covariat
  449.692 not equal to cav5cov.msm$minus2loglik.
  1/1 mismatches
  [1] 450 - 458 == -7.82
  
  -- 5. Failure: piecewise constant intensities with pci, with uncentered covariat
  449.692 not equal to cav5cov.msm$minus2loglik.
  1/1 mismatches
  [1] 450 - 458 == -7.82
  
  == testthat results  ===========================================================
  OK: 462 SKIPPED: 2 FAILED: 5
  1. Failure: Information matrix (@test_deriv.r#138) 
  2. Failure: piecewise constant intensities with pci, with other covariates (@test_models.r#202) 
  3. Failure: piecewise constant intensities with pci, with other covariates (@test_models.r#210) 
  4. Failure: piecewise constant intensities with pci, with uncentered covariates (@test_models.r#218) 
  5. Failure: piecewise constant intensities with pci, with uncentered covariates (@test_models.r#226) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'test_base.R' [49s]
Running the tests in 'tests/test_base.R' failed.
Complete output:
  > library(testthat)
  > test_check("msm")
  Loading required package: msm
  -- 1. Failure: Information matrix (@test_deriv.r#138)  -------------------------
  c(0.88475550512612, 0.202501688704573, -0.474183198550202) not equal to tm$paramdata$info[1:3].
  3/3 mismatches (average diff: 0.284)
  [1]  0.885 -  1.0455 == -0.161
  [2]  0.203 -  0.0872 ==  0.115
  [3] -0.474 - -1.0490 ==  0.575
  
  -- 2. Failure: piecewise constant intensities with pci, with other covariates (@
  448.1228 not equal to cav5cov.msm$minus2loglik.
  1/1 mismatches
  [1] 448 - 456 == -7.79
  
  -- 3. Failure: piecewise constant intensities with pci, with other covariates (@
  448.1228 not equal to cav5cov.msm$minus2loglik.
  1/1 mismatches
  [1] 448 - 456 == -7.79
  
  -- 4. Failure: piecewise constant intensities with pci, with uncentered covariat
  449.692 not equal to cav5cov.msm$minus2loglik.
  1/1 mismatches
  [1] 450 - 458 == -7.82
  
  -- 5. Failure: piecewise constant intensities with pci, with uncentered covariat
  449.692 not equal to cav5cov.msm$minus2loglik.
  1/1 mismatches
  [1] 450 - 458 == -7.82
  
  == testthat results  ===========================================================
  OK: 462 SKIPPED: 2 FAILED: 5
  1. Failure: Information matrix (@test_deriv.r#138) 
  2. Failure: piecewise constant intensities with pci, with other covariates (@test_models.r#202) 
  3. Failure: piecewise constant intensities with pci, with other covariates (@test_models.r#210) 
  4. Failure: piecewise constant intensities with pci, with uncentered covariates (@test_models.r#218) 
  5. Failure: piecewise constant intensities with pci, with uncentered covariates (@test_models.r#226) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.4Mb
    libs   1.5Mb
Running 'testthat.R' [78s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(myTAI)
  > 
  > test_check("myTAI")
  
  
  
  -- 1. Failure: PlotEnrichment() computes correct values... (@test-PlotEnrichment
  round(...) not equal to round(c(1, 1, 0.2406024, 1, 1, 0.4215795, 1), 5).
  5/7 mismatches (average diff: 0.519)
  [1] 0.525 - 1.000 == -0.475
  [3] 0.553 - 0.241 ==  0.313
  [5] 0.350 - 1.000 == -0.650
  [6] 1.000 - 0.422 ==  0.578
  [7] 0.422 - 1.000 == -0.578
  
  == testthat results  ===========================================================
  OK: 265 SKIPPED: 1 FAILED: 1
  1. Failure: PlotEnrichment() computes correct values... (@test-PlotEnrichment.R#271) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [67s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(myTAI)
  > 
  > test_check("myTAI")
  
  
  
  -- 1. Failure: PlotEnrichment() computes correct values... (@test-PlotEnrichment
  round(...) not equal to round(c(1, 1, 0.2406024, 1, 1, 0.4215795, 1), 5).
  5/7 mismatches (average diff: 0.519)
  [1] 0.525 - 1.000 == -0.475
  [3] 0.553 - 0.241 ==  0.313
  [5] 0.350 - 1.000 == -0.650
  [6] 1.000 - 0.422 ==  0.578
  [7] 0.422 - 1.000 == -0.578
  
  == testthat results  ===========================================================
  OK: 265 SKIPPED: 1 FAILED: 1
  1. Failure: PlotEnrichment() computes correct values... (@test-PlotEnrichment.R#271) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
See 'd:/Rcompile/CRANpkg/local/3.6/NanoStringNorm.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
See 'd:/Rcompile/CRANpkg/local/3.6/NAPPA.Rcheck/00install.out' for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
File 'NeatMap/libs/i386/NeatMap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'nMDS_R.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'nMDS_R.o'
File 'NeatMap/libs/x64/NeatMap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'nMDS_R.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'nMDS_R.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    CppCode   2.5Mb
    R         5.7Mb
    include   5.7Mb
    libs      1.8Mb
    tests     1.5Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.2Mb
Running examples in 'nsrr-Ex.R' failed
The error most likely occurred in:

> ### Name: nsrr_datasets
> ### Title: NSRR data sets
> ### Aliases: nsrr_datasets nsrr_dataset_files
> 
> ### ** Examples
> 
> df = nsrr_datasets()
Error: lexical error: invalid char in json text.
                                       <html>  <head><title>504 Gatewa
                     (right here) ------^
Execution halted
Running 'testthat.R' [138s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(nsrr)
  > 
  > test_check("nsrr")
  -- 1. Error: Testing if data sets returns a data.frame if not authenticated (@te
  lexical error: invalid char in json text.
                                         <html>  <head><title>502 Bad Ga
                       (right here) ------^
  1: nsrr_datasets(NULL) at testthat/test-token.R:7
  2: jsonlite::fromJSON(x, flatten = TRUE)
  3: parse_and_simplify(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  4: parseJSON(txt, bigint_as_char)
  5: parse_string(txt, bigint_as_char)
  
  == testthat results  ===========================================================
  OK: 0 SKIPPED: 1 FAILED: 1
  1. Error: Testing if data sets returns a data.frame if not authenticated (@test-token.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'downloading_data_nsrr.Rmd' using rmarkdown
Quitting from lines 30-32 (downloading_data_nsrr.Rmd) 
Error: processing vignette 'downloading_data_nsrr.Rmd' failed with diagnostics:
Please install xml2 package
--- failed re-building 'downloading_data_nsrr.Rmd'

SUMMARY: processing the following file failed:
  'downloading_data_nsrr.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   2.5Mb
installed size is 38.9Mb
  sub-directories of 1Mb or more:
    extdata  38.9Mb
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.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
File 'obliclus/libs/i386/obliclus.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'random_cluster_C.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'random_cluster_C.o'
File 'obliclus/libs/x64/obliclus.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'random_cluster_C.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'random_cluster_C.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.5Mb
    help   2.5Mb
    libs   2.3Mb
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.
MLparameters: no visible global function definition for 'optim'
comp.freq: no visible global function definition for 'x11'
comp.freq: no visible global function definition for 'par'
comp.freq: no visible global function definition for 'plot'
Undefined global functions or variables:
  optim par plot x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "optim")
to your NAMESPACE file.
Package suggested but not available for checking: 'unix'
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    R        2.5Mb
    libs     7.1Mb
    models   4.9Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.6Mb
Running 'anova.R' [3s]
  Running 'clm.fit.R' [3s]
  Running 'clm.formula.R' [3s]
  Running 'clmm.R' [9s]
  Running 'clmm.control.R' [2s]
  Running 'clmm.formula.R' [5s]
  Running 'confint.R' [4s]
  Running 'nominal.test.R' [6s]
  Running 'test-all.R' [24s]
  Running 'test.clm.Theta.R' [4s]
  Running 'test.clm.convergence.R' [3s]
  Running 'test.clm.flex.link.R' [3s]
  Running 'test.clm.model.matrix.R' [3s]
  Running 'test.clm.predict.R' [3s]
  Running 'test.clm.profile.R' [3s]
  Running 'test.clm.single.anova.R' [3s]
  Running 'test.general.R' [0s]
  Running 'test.makeThresholds.R' [2s]
  Running 'test.sign.R' [3s]
  Running 'test0weights.R' [4s]
  Running 'testAnova.clm2.R' [3s]
  Running 'testCLM.R' [4s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > 
  > if(require(testthat) && require(ordinal)) {
  +     test_check("ordinal")
  + }
  Loading required package: testthat
  Loading required package: ordinal
  -- 1. Failure: clm gives contrast warnings when it should (@test-contrasts.R#11)
  givesWarnings(...) isn't false.
  
  -- 2. Failure: clm gives contrast warnings when it should (@test-contrasts.R#15)
  givesWarnings(...) isn't false.
  
  -- 3. Failure: clm gives contrast warnings when it should (@test-contrasts.R#19)
  givesWarnings(...) isn't false.
  
  -- 4. Failure: clm gives contrast warnings when it should (@test-contrasts.R#23)
  givesWarnings(...) isn't false.
  
  == testthat results  ===========================================================
  OK: 80 SKIPPED: 0 FAILED: 4
  1. Failure: clm gives contrast warnings when it should (@test-contrasts.R#11) 
  2. Failure: clm gives contrast warnings when it should (@test-contrasts.R#15) 
  3. Failure: clm gives contrast warnings when it should (@test-contrasts.R#19) 
  4. Failure: clm gives contrast warnings when it should (@test-contrasts.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'anova.R' [3s]
  Running 'clm.fit.R' [3s]
  Running 'clm.formula.R' [3s]
  Running 'clmm.R' [10s]
  Running 'clmm.control.R' [3s]
  Running 'clmm.formula.R' [5s]
  Running 'confint.R' [5s]
  Running 'nominal.test.R' [7s]
  Running 'test-all.R' [28s]
  Running 'test.clm.Theta.R' [4s]
  Running 'test.clm.convergence.R' [3s]
  Running 'test.clm.flex.link.R' [3s]
  Running 'test.clm.model.matrix.R' [3s]
  Running 'test.clm.predict.R' [3s]
  Running 'test.clm.profile.R' [3s]
  Running 'test.clm.single.anova.R' [4s]
  Running 'test.general.R' [1s]
  Running 'test.makeThresholds.R' [3s]
  Running 'test.sign.R' [4s]
  Running 'test0weights.R' [4s]
  Running 'testAnova.clm2.R' [4s]
  Running 'testCLM.R' [4s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > 
  > if(require(testthat) && require(ordinal)) {
  +     test_check("ordinal")
  + }
  Loading required package: testthat
  Loading required package: ordinal
  -- 1. Failure: clm gives contrast warnings when it should (@test-contrasts.R#11)
  givesWarnings(...) isn't false.
  
  -- 2. Failure: clm gives contrast warnings when it should (@test-contrasts.R#15)
  givesWarnings(...) isn't false.
  
  -- 3. Failure: clm gives contrast warnings when it should (@test-contrasts.R#19)
  givesWarnings(...) isn't false.
  
  -- 4. Failure: clm gives contrast warnings when it should (@test-contrasts.R#23)
  givesWarnings(...) isn't false.
  
  == testthat results  ===========================================================
  OK: 80 SKIPPED: 0 FAILED: 4
  1. Failure: clm gives contrast warnings when it should (@test-contrasts.R#11) 
  2. Failure: clm gives contrast warnings when it should (@test-contrasts.R#15) 
  3. Failure: clm gives contrast warnings when it should (@test-contrasts.R#19) 
  4. Failure: clm gives contrast warnings when it should (@test-contrasts.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [32s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(origami)
  origami: Generalized Cross-Validation Framework
  Version: 1.0.0
  > library(data.table)
  > test_check("origami")
  -- 1. Failure: CV MSE matches previous value (@test-overall.R#36)  -------------
  `cv_MSE` not equal to 13.32.
  1/1 mismatches
  [1] 14.1 - 13.3 == 0.791
  
  == testthat results  ===========================================================
  OK: 33 SKIPPED: 1 FAILED: 1
  1. Failure: CV MSE matches previous value (@test-overall.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
File 'OriGen/libs/i386/OriGen.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'OriGen.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'OriGen.o'
File 'OriGen/libs/x64/OriGen.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'OriGen.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'OriGen.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
Package suggested but not available for checking: 'Rcplex'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   1.8Mb
Running 'testthat_chi2.R' [6s]
  Running 'testthat_extractSubTree.R' [23s]
  Running 'testthat_pacotestRegressionTests.R' [7s]
  Running 'testthat_pacotestRvineSeqRegressionTests.R' [65s]
  Running 'testthat_pacotestRvineSingleCopulaRegressionTests.R' [217s]
Running the tests in 'tests/testthat_pacotestRvineSeqRegressionTests.R' failed.
Complete output:
  > 
  > library("testthat")
  > library("pacotest")
  > 
  > test_check("pacotest", filter = "pacotestRvineSeqRegressionTests")
  -- 1. Failure: pacotestRvineSeq7 (@test-pacotestRvineSeqRegressionTests.R#194)  
  resPacotestComputed[iTest, 1:3] not equal to hardCodedResPacotestRvineSeq[iTest, 1:3].
  1/3 mismatches
  [2] 0.768 - 0.755 == 0.013
  
  == testthat results  ===========================================================
  OK: 4 SKIPPED: 5 FAILED: 1
  1. Failure: pacotestRvineSeq7 (@test-pacotestRvineSeqRegressionTests.R#194) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat_chi2.R' [7s]
  Running 'testthat_extractSubTree.R' [26s]
  Running 'testthat_pacotestRegressionTests.R' [8s]
  Running 'testthat_pacotestRvineSeqRegressionTests.R' [68s]
  Running 'testthat_pacotestRvineSingleCopulaRegressionTests.R' [216s]
Running the tests in 'tests/testthat_pacotestRvineSeqRegressionTests.R' failed.
Complete output:
  > 
  > library("testthat")
  > library("pacotest")
  > 
  > test_check("pacotest", filter = "pacotestRvineSeqRegressionTests")
  -- 1. Failure: pacotestRvineSeq7 (@test-pacotestRvineSeqRegressionTests.R#194)  
  resPacotestComputed[iTest, 1:3] not equal to hardCodedResPacotestRvineSeq[iTest, 1:3].
  1/3 mismatches
  [2] 0.768 - 0.755 == 0.013
  
  == testthat results  ===========================================================
  OK: 4 SKIPPED: 5 FAILED: 1
  1. Failure: pacotestRvineSeq7 (@test-pacotestRvineSeqRegressionTests.R#194) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(padr)
  > 
  > test_check("padr")
  -- 1. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#
  fill_by_function(x_df, y1)$y1 %>% median not equal to 14.77.
  1/1 mismatches
  [1] 14.8 - 14.8 == 0.04
  
  -- 2. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#
  fill_by_function(x_df, y1, y2)$y1 %>% median not equal to 14.77.
  1/1 mismatches
  [1] 14.8 - 14.8 == 0.04
  
  -- 3. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#
  fill_by_function(x_df, y1, y2)$y2 %>% median not equal to 22.765.
  1/1 mismatches
  [1] 25.3 - 22.8 == 2.5
  
  -- 4. Failure: fill_by_prevalent gives expected outcomes (@test_fill_functions.R
  `fill_by_prevalent(x_df, y1)` did not throw an error.
  
  == testthat results  ===========================================================
  OK: 584 SKIPPED: 1 FAILED: 4
  1. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#36) 
  2. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#37) 
  3. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#38) 
  4. Failure: fill_by_prevalent gives expected outcomes (@test_fill_functions.R#48) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(padr)
  > 
  > test_check("padr")
  -- 1. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#
  fill_by_function(x_df, y1)$y1 %>% median not equal to 14.77.
  1/1 mismatches
  [1] 14.8 - 14.8 == 0.04
  
  -- 2. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#
  fill_by_function(x_df, y1, y2)$y1 %>% median not equal to 14.77.
  1/1 mismatches
  [1] 14.8 - 14.8 == 0.04
  
  -- 3. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#
  fill_by_function(x_df, y1, y2)$y2 %>% median not equal to 22.765.
  1/1 mismatches
  [1] 25.3 - 22.8 == 2.5
  
  -- 4. Failure: fill_by_prevalent gives expected outcomes (@test_fill_functions.R
  `fill_by_prevalent(x_df, y1)` did not throw an error.
  
  == testthat results  ===========================================================
  OK: 584 SKIPPED: 1 FAILED: 4
  1. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#36) 
  2. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#37) 
  3. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#38) 
  4. Failure: fill_by_prevalent gives expected outcomes (@test_fill_functions.R#48) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(palasso)
  > 
  > testthat::test_check("palasso")
  -- 1. Failure: deviance stats (@test.R#146)  -----------------------------------
  `x` isn't true.
  
  -- 2. Error: coef stats (@test.R#126)  -----------------------------------------
  attempt to select less than one element in get1index
  1: coef(fit, model = "standard_xz", s = 0) at testthat/test.R:126
  2: coef.palasso(fit, model = "standard_xz", s = 0)
  3: subset.palasso(x = object, model = model, max = max)
  
  -- 3. Error: deviance stats (@test.R#142)  -------------------------------------
  attempt to select less than one element in get1index
  1: deviance(fit, model = "standard_xz") at testthat/test.R:142
  2: deviance.palasso(fit, model = "standard_xz")
  3: subset.palasso(x = object, model = model, max = max)
  
  -- 4. Error: logLik stats (@test.R#150)  ---------------------------------------
  attempt to select less than one element in get1index
  1: logLik(fit, model = "standard_xz") at testthat/test.R:150
  2: logLik.palasso(fit, model = "standard_xz")
  3: subset.palasso(x = object, model = model, max = max)
  
  == testthat results  ===========================================================
  OK: 2107 SKIPPED: 2 FAILED: 4
  1. Failure: deviance stats (@test.R#146) 
  2. Error: coef stats (@test.R#126) 
  3. Error: deviance stats (@test.R#142) 
  4. Error: logLik stats (@test.R#150) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    data      2.5Mb
    doc       1.3Mb
    extdata   9.5Mb
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > std_getwd <- function() 
  + {
  +   pwd <- getwd()
  +   # Enforce upper case Windows drive letters
  +   substring(pwd, 1, 1) <- toupper(substring(pwd, 1, 1))
  +   pwd
  + }
  > 
  > test_check("pathological")
  Loading required package: pathological
  -- 1. Failure: decompose_path handles paths with a unicode directory name. (@tes
  actual$dirname not equal to expected$dirname.
  1/1 mismatches
  x[1]: "D:/Rcompile/CRANpkg/local/3.6/pathological.Rcheck/tests/testthat/CRAN"
  y[1]: "D:/Rcompile/CRANpkg/local/3.6/pathological.Rcheck/tests/testthat/CRAN"
  
  -- 2. Failure: standardize_path works with missing files with ./ prefix (@test_s
  standardize_path(x) not equal to `expected`.
  1/2 mismatches
  x[1]: "D:/RCompile/CRANpkg/local/3.6/pathological.Rcheck/tests/testthat/test_dec
  x[1]: ompose_path.R"
  y[1]: "D:/Rcompile/CRANpkg/local/3.6/pathological.Rcheck/tests/testthat/test_dec
  y[1]: ompose_path.R"
  
  == testthat results  ===========================================================
  OK: 186 SKIPPED: 18 FAILED: 2
  1. Failure: decompose_path handles paths with a unicode directory name. (@test_decompose_path.R#466) 
  2. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  
  Error: testthat unit tests failed
  Execution halted
Not exits: C:/Program Files/netCDF 4.3.2
Not exits: C:/Program Files/netCDF 4.3.2/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcp100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcr100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/zlib.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5_hl.dll
Not exits: C:/Program Files/netCDF 4.3.2/bin/netcdf.dll
===== WARNING =====
- netCDF 4.3.2 may not install at compile time.
- Environment variables may not be correct at compile and run time.
- pbdNCDF4 binary may not link with netCDF.
- Please consider to rebuild from source.
===================
Not exits: C:/Program Files/netCDF 4.3.2
Not exits: C:/Program Files/netCDF 4.3.2/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcp100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcr100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/zlib.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5_hl.dll
Not exits: C:/Program Files/netCDF 4.3.2/bin/netcdf.dll
===== WARNING =====
- netCDF 4.3.2 may not install at compile time.
- Environment variables may not be correct at compile and run time.
- pbdNCDF4 binary may not link with netCDF.
- Please consider to rebuild from source.
===================
get.sysenv: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    lib    6.6Mb
    libs   5.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.4Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   2.7Mb
    libs      1.8Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.1Mb
    libs   2.3Mb
Running examples in 'pcalg-Ex.R' failed
The error most likely occurred in:

> ### Name: backdoor
> ### Title: Find Set Satisfying the Generalized Backdoor Criterion (GBC)
> ### Aliases: backdoor
> ### Keywords: multivariate models graphs
> 
> ### ** Examples
> 
> #####################################################################
> ##DAG
> #####################################################################
> ## Simulate the true DAG
> set.seed(123)
> p <- 7
> myDAG <- randomDAG(p, prob = 0.2) ## true DAG
> 
> ## Extract the adjacency matrix of the true DAG
> true.amat <- (amat <- as(myDAG, "matrix")) != 0 # TRUE/FALSE <==> 1/0
> print.table(1*true.amat, zero.=".") # "visualization"
  1 2 3 4 5 6 7
1 . . . 1 . . .
2 . . . 1 . . 1
3 . . . . . . 1
4 . . . . 1 . .
5 . . . . . . 1
6 . . . . . . .
7 . . . . . . .
> 
> ## Compute set satisfying the GBC:
> backdoor(true.amat, 5, 7, type="dag")
[1] 4
> ## Don't show: 
> stopifnot(backdoor(true.amat, 5, 7, type="dag") == 3)
Error: backdoor(true.amat, 5, 7, type = "dag") == 3 is not TRUE
Execution halted
Running examples in 'pcnetmeta-Ex.R' failed
The error most likely occurred in:

> ### Name: absolute.plot
> ### Title: Plotting Treatment-Specific 95% Credible Intervals
> ### Aliases: absolute.plot
> 
> ### ** Examples
> 
> data(smoke)
> # increase n.iter to reach convergence
> # increase n.adapt to enhance efficiency
> set.seed(1234)
> nma.out <- nma.ab.bin(s.id, t.id, r, n, data = smoke,
+   trtname = c("NC", "SH", "IC", "GC"), param= "AR",
+   model = "het_cor", n.adapt = 400, n.iter = 100, n.chains = 1)
Start running MCMC...
Compiling model graph
   Resolving undeclared variables
   Allocating nodes
Graph information:
   Observed stochastic nodes: 50
   Unobserved stochastic nodes: 29
   Total graph size: 611

Initializing model

> absolute.plot(nma.out)
The absolute plot is saved in your working directory:
d:/Rcompile/CRANpkg/local/3.6/pcnetmeta.Rcheck
> absolute.plot(nma.out, alphabetic = FALSE)
The absolute plot is saved in your working directory:
d:/Rcompile/CRANpkg/local/3.6/pcnetmeta.Rcheck
> 
> 
> 
> cleanEx()
Error: connections left open:
	modelstring (textConnection)
Execution halted
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs   13.3Mb
    share  11.9Mb
Package suggested but not available for checking: 'faahKO'
Malformed Title field: should not end in a period.
'LinkingTo' for 'ggplot2' is unused as it has no 'include' directory
Running examples in 'penDvine-Ex.R' failed
The error most likely occurred in:

> ### Name: penDvine-package
> ### Title: The package 'penDvine' offers routines for estimating densities
> ###   and copula distribution of D-vines.
> ### Aliases: penDvine-package
> 
> ### ** Examples
> 
> #This examples describes the estimation of a D-vine to winddata,
> #available in this package. After the margins are prepared, we estimate a
> #D-vine using B-splines with 9 (K+1) marginal knots and penalizing second (m=2)
> #order differences (pen=1) of the basis coefficients.
> 
> data(Winddata)
> ex.data<-Winddata[c(1:100),c(1:4)] #examplary subdata for fast calculation
> wind.example<-Dvine(ex.data,K=7,pen=1,lambda=100,order.Dvine=FALSE,base="B-spline",m=2,cores=2)
>   
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11879 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11879 (sockconn)
Execution halted
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > ## Test `permute` using the `testthat` package
  > 
  > ## Setup
  > library("testthat")
  > library("permute")
  > 
  > ## Runs the tests in inst/tests
  > test_check("permute")
  -- 1. Failure: shuffle() works for non-contigous blocks of samples (@test-shuffl
  `x` not identical to `expected`.
  10/20 mismatches (average diff: 3)
  [3]   4 -  1 ==  3
  [4]   1 -  4 == -3
  [7]   8 -  5 ==  3
  [8]   5 -  8 == -3
  [11] 12 -  9 ==  3
  [12]  9 - 12 == -3
  [15] 16 - 13 ==  3
  [16] 13 - 16 == -3
  [19] 20 - 17 ==  3
  ...
  
  -- 2. Failure: shuffle() works for non-contigous blocks of samples (@test-shuffl
  `x` not identical to `expected`.
  10 string mismatches
  
  == testthat results  ===========================================================
  OK: 298 SKIPPED: 0 FAILED: 2
  1. Failure: shuffle() works for non-contigous blocks of samples (@test-shuffle.R#40) 
  2. Failure: shuffle() works for non-contigous blocks of samples (@test-shuffle.R#42) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > suppressPackageStartupMessages(library(phangorn))
  > 
  > test_check("phangorn")
  loglik: -11409.87 --> -11409.87 
  -- 1. Failure: SPR distance (@test_treedist.R#100)  ----------------------------
  SPR.dist(tree1, trees) not equal to 1:5.
  1/5 mismatches
  [2] 1 - 2 == -1
  
  == testthat results  ===========================================================
  OK: 120 SKIPPED: 28 FAILED: 1
  1. Failure: SPR distance (@test_treedist.R#100) 
  
  Error: testthat unit tests failed
  Execution halted
File 'PhaseType/libs/i386/PhaseType.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'LJMA_arms.o'
File 'PhaseType/libs/x64/PhaseType.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'LJMA_arms.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Running examples in 'phylosim-Ex.R' failed
The error most likely occurred in:

> ### Name: getLogLevel.PhyloSim
> ### Title: Get the log level from a PhyloSim object
> ### Aliases: getLogLevel.PhyloSim PhyloSim.getLogLevel
> ###   getLogLevel,PhyloSim-method
> 
> ### ** Examples
> 
> 	# Create a PhyloSim object
> 	sim<-PhyloSim();
> 	# get/set log level
> 	getLogLevel(sim)
[1] -1
> 	setLogLevel(sim,0)
[1] 0
> 	# set/get log level via virtual field
> 	sim$logLevel<- -1
> 	sim$logLevel
[1] -1
> 	# clean up
> 	unlink(sim$logFile)
>  
> 
> 
> cleanEx()
Error: connections left open:
	PhyloSim_Anonymous_283419688.log (file)
Execution halted
Running examples in 'plater-Ex.R' failed
The error most likely occurred in:

> ### Name: add_plate
> ### Title: Read a plater-formatted file and combine it with an existing
> ###   data frame.
> ### Aliases: add_plate
> 
> ### ** Examples
> 
> # Part of the data is tidy
> file <- system.file("extdata", "example-2-part-A.csv", package = "plater")
> data <- read.csv(file)
> 
> # Part of the data is plate-shaped
> plate_shaped <- system.file("extdata", "example-2-part-B.csv", package = "plater")
> 
> # Combine the two
> data <- add_plate(
+    data = data, 
+    file = plate_shaped,
+    well_ids_column = "Wells")
> 
> # Now data are tidy
> head(data)
  Wells Killing Drug Concentration Bacteria
1   A01      98    A       100.000  E. coli
2   A02      95    A        20.000  E. coli
3   A03      92    A         4.000  E. coli
4   A04      41    A         0.800  E. coli
5   A05      17    A         0.160  E. coli
6   A06       2    A         0.032  E. coli
> 
> 
> 
> cleanEx()
Error: connections left open:
	plate (textConnection)
	plate (textConnection)
	plate (textConnection)
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.0Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Running 'test-all.R' [14s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > options(poppr.debug = TRUE)
  > test_check("poppr")
  Loading required package: poppr
  Loading required package: adegenet
  Loading required package: ade4
  
     /// adegenet 2.1.1 is loaded ////////////
  
     > overview: '?adegenet'
     > tutorials/doc/questions: 'adegenetWeb()' 
     > bug reports/feature requests: adegenetIssues()
  
  
  This is poppr version 2.8.1. To get started, type package?poppr
  OMP parallel support: available
  -- 1. Failure: rrmlg produces the correct mlgs (@test-round-robin.R#24)  -------
  `rrx_m` not equivalent to `mlg_truth`.
  11/15 mismatches (average diff: 1.73)
  [2]  3 - 2 ==  1
  [3]  2 - 3 == -1
  [5]  4 - 1 ==  3
  [6]  1 - 2 == -1
  [7]  3 - 4 == -1
  [9]  1 - 3 == -2
  [10] 4 - 1 ==  3
  [12] 4 - 3 ==  1
  [13] 3 - 2 ==  1
  ...
  
  == testthat results  ===========================================================
  OK: 308 SKIPPED: 186 FAILED: 1
  1. Failure: rrmlg produces the correct mlgs (@test-round-robin.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'test-all.R' [16s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > options(poppr.debug = TRUE)
  > test_check("poppr")
  Loading required package: poppr
  Loading required package: adegenet
  Loading required package: ade4
  
     /// adegenet 2.1.1 is loaded ////////////
  
     > overview: '?adegenet'
     > tutorials/doc/questions: 'adegenetWeb()' 
     > bug reports/feature requests: adegenetIssues()
  
  
  This is poppr version 2.8.1. To get started, type package?poppr
  OMP parallel support: available
  -- 1. Failure: rrmlg produces the correct mlgs (@test-round-robin.R#24)  -------
  `rrx_m` not equivalent to `mlg_truth`.
  11/15 mismatches (average diff: 1.73)
  [2]  3 - 2 ==  1
  [3]  2 - 3 == -1
  [5]  4 - 1 ==  3
  [6]  1 - 2 == -1
  [7]  3 - 4 == -1
  [9]  1 - 3 == -2
  [10] 4 - 1 ==  3
  [12] 4 - 3 ==  1
  [13] 3 - 2 ==  1
  ...
  
  == testthat results  ===========================================================
  OK: 308 SKIPPED: 186 FAILED: 1
  1. Failure: rrmlg produces the correct mlgs (@test-round-robin.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'popRange-Ex.R' failed
The error most likely occurred in:

> ### Name: popRangeSim
> ### Title: popRangeSim
> ### Aliases: popRangeSim
> 
> ### ** Examples
>  
> ## Example: In this scenario, we are simulating a 3x3 grid of populations for 50 
> ## generations. Each population starts with 100 diploid individuals. Each individual 
> ## has a 0.01 probability of migrating away from their populations. There are 100 
> ## SNPs that all have a starting frequency of 0.5, and the program outputs the standard 
> ## "results" file, as well as a PLINK file. 
> 
> ## Commands
> 
> mat = matrix(1,nrow=3,ncol=3) 
> popRangeSim(world = mat, popSize = 100, diploid = TRUE, nGens = 50,
+               mig = 0.01, SNP_model = 0, nSNPs = 100, SNPs_starting_freq = 0.5, 
+               outfile= "outFile1", PLINK=TRUE)
Error in find_python_cmd(minimum_version = minimum_version, maximum_version = maximum_version,  : 
  Couldn't find a sufficient Python binary. If you haven't installed the Python dependency yet please do so. If you have but it isn't on the system path (as is default on Windows) please add it to path or set options('python_cmd'='/path/to/binary')  or set the PYTHON, PYTHON2, or PYTHON3 environmental variables. Python must be at least version 2.7 Python must be at most version 3.4 Python must have access to the modules: numpy
[1] "Could not find an acceptable version of python with numpy installed. This should be able to locate python \n      anywhere on your computer, but perhaps try adding python to your PATH if you think this message is an error."
Error in popRangeSim(world = mat, popSize = 100, diploid = TRUE, nGens = 50,  : 
  
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
File 'powell/libs/i386/powell.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'powell.o'
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
    Object: 'powell.o'
File 'powell/libs/x64/powell.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'powell.o'
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
    Object: 'powell.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Error(s) in re-building vignettes:
--- re-building 'intro_pfit.Rmd' using rmarkdown
PP package calling ...
Follow this project on github: https://github.com/manuelreif/PP.git
Quitting from lines 131-155 (intro_pfit.Rmd) 
Error: processing vignette 'intro_pfit.Rmd' failed with diagnostics:
'x' contains missing values
--- failed re-building 'intro_pfit.Rmd'

--- re-building 'intro_pp.Rmd' using rmarkdown
--- finished re-building 'intro_pp.Rmd'

--- re-building 'ppass_par_and_fit.Rmd' using rmarkdown
--- finished re-building 'ppass_par_and_fit.Rmd'

SUMMARY: processing the following file failed:
  'intro_pfit.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   2.6Mb
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(probably)
  
  Attaching package: 'probably'
  
  The following objects are masked from 'package:base':
  
      as.factor, as.ordered
  
  > 
  > test_check("probably")
  -- 1. Failure: class_pred printing (@test-class-pred.R#408)  -------------------
  `cat_levels\(cp\)` does not match "10 Levels: dkkjddgmgwbludofdtxj grkuclzxxedqirieucmn \\.\\.\\. xsqzrsophdzxruamtfig".
  Actual value: "10 Levels: dahtypxvkpthcdtlvqjt hzgjisdnqkgulojmgiij \.\.\. zptfkhvvgpqvrqbdmevs"
  
  == testthat results  ===========================================================
  OK: 116 SKIPPED: 0 FAILED: 1
  1. Failure: class_pred printing (@test-class-pred.R#408) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc           6.5Mb
    help          2.0Mb
    htmlwidgets   2.5Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    extdata   6.4Mb
    libs      1.6Mb
Package suggested but not available for checking: 'qtbase'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.3Mb
Running examples in 'psymonitor-Ex.R' failed
The error most likely occurred in:

> ### Name: disp
> ### Title: Generate a table with identified bubble/crisis periods
> ### Aliases: disp
> 
> ### ** Examples
> 
> data(spread)
> 
> y        <- spread$value[150:200]
> obs      <- length(y)
> swindow0 <- floor(obs*(0.01 + 1.8/sqrt(obs)))
> dim      <- obs - swindow0 + 1
> Tb       <- 24 + swindow0 - 1
> 
> # Estimate PSY statistics and CVs
> bsadf          <- PSY(y, swindow0)
> quantilesBsadf <- cvPSYwmboot(y, swindow0, Tb=Tb, nboot = 49, nCores = 2)
> quantile95     <- quantilesBsadf %*% matrix(1, nrow = 1, ncol = dim)
> 
> # locate bubble/crisis dates
> ind95        <- (bsadf > t(quantile95[2, ])) * 1
> monitorDates <- spread$date[swindow0:obs]
> OT           <- locate(ind95, monitorDates)
Warning: No bubble or crisis periods found
> 
> # Show bubble/crisis periods
> disp(OT, obs)
Error: No bubble or crisis periods found.
Execution halted
Running examples in 'pxweb-Ex.R' failed
The error most likely occurred in:

> ### Name: pxweb_data_comments
> ### Title: Construct a 'pxweb_data_comments' object.
> ### Aliases: pxweb_data_comments pxweb_data_comments.pxweb_data
> ### Keywords: internal
> 
> ### ** Examples
> 
> url <- "http://api.scb.se/OV0104/v1/doris/en/ssd/BE/BE0101/BE0101A/BefolkningNy"
> json_query <- 
+   file.path(system.file(package = "pxweb"), "extdata", "examples", "json_query_example.json")
> pxd <- pxweb_get(url = url, query = json_query)
Error in pxweb_advanced_get(url = url, query = query, verbose = verbose) : 
  Not Found (HTTP 404).
Calls: pxweb_get ... pxweb_advanced_get -> pxweb_get -> pxweb_advanced_get -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building 'pxweb.Rmd' using rmarkdown
pxweb: R tools for PX-WEB API.
Copyright (C) 2014-2018 Mans Magnusson, Leo Lahti et al.
https://github.com/ropengov/pxweb

Quitting from lines 137-140 (pxweb.Rmd) 
Error: processing vignette 'pxweb.Rmd' failed with diagnostics:
Not Found (HTTP 404).
--- failed re-building 'pxweb.Rmd'

SUMMARY: processing the following file failed:
  'pxweb.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data  11.8Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.6Mb
    doc       2.9Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   1.3Mb
    libs   3.3Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   2.1Mb
Running 'testthat.R' [55s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(Quartet)
  > 
  > test_check("Quartet")
  -- 1. Failure: CompareSplits works (@test-PartitionDistance.R#27)  -------------
  c(N = 6, P1 = 3L, P2 = 3L, s = 3, d1 = 0, d2 = 0, r1 = 0, r2 = 0) not equal to CompareSplits(splits9Fewer, splits9).
  4/8 mismatches (average diff: 3)
  [1] 6 -  9 == -3
  [2] 3 -  6 == -3
  [4] 3 -  6 == -3
  [6] 0 - -3 ==  3
  
  == testthat results  ===========================================================
  OK: 146 SKIPPED: 0 FAILED: 1
  1. Failure: CompareSplits works (@test-PartitionDistance.R#27) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [36s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(Quartet)
  > 
  > test_check("Quartet")
  -- 1. Failure: CompareSplits works (@test-PartitionDistance.R#27)  -------------
  c(N = 6, P1 = 3L, P2 = 3L, s = 3, d1 = 0, d2 = 0, r1 = 0, r2 = 0) not equal to CompareSplits(splits9Fewer, splits9).
  4/8 mismatches (average diff: 3)
  [1] 6 -  9 == -3
  [2] 3 -  6 == -3
  [4] 3 -  6 == -3
  [6] 0 - -3 ==  3
  
  == testthat results  ===========================================================
  OK: 146 SKIPPED: 0 FAILED: 1
  1. Failure: CompareSplits works (@test-PartitionDistance.R#27) 
  
  Error: testthat unit tests failed
  Execution halted
File 'QUIC/libs/i386/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'
File 'QUIC/libs/x64/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
File 'qVarSel/libs/i386/qVarSel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'qVarSelH.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'qVarSelH.o'
File 'qVarSel/libs/x64/qVarSel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'qVarSelH.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'qVarSelH.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(qwraps2)
  > 
  > test_check("qwraps2")
  -- 1. Failure: Boot Strap (@test-confusion_matrix.R#15)  -----------------------
  round(con_mat_boot$stats[, "Boot Est"], 3) not equivalent to c(0.573, 0.669, 0.532, 0.382, 0.788).
  5/5 mismatches (average diff: 0.003)
  [1] 0.570 - 0.573 == -0.003
  [2] 0.670 - 0.669 ==  0.001
  [3] 0.527 - 0.532 == -0.005
  [4] 0.377 - 0.382 == -0.005
  [5] 0.789 - 0.788 ==  0.001
  
  == testthat results  ===========================================================
  OK: 49 SKIPPED: 0 FAILED: 1
  1. Failure: Boot Strap (@test-confusion_matrix.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin      9.3Mb
Running examples in 'R2HTML-Ex.R' failed
The error most likely occurred in:

> ### Name: HTM2clip
> ### Title: Wrapper around HTML() to save output to the clipboard
> ### Aliases: HTML2clip
> ### Keywords: print IO file
> 
> ### ** Examples
> 
> if (.Platform$OS == "windows")
+ 	HTML2clip(summary(lm(rating ~., attitude)))
> 
> 
> 
> cleanEx()
Error: connections left open:
	clipboard (clipboard)
Execution halted
Packages suggested but not available for checking: 'rcom', 'RDCOMClient'
'library' or 'require' calls in package code:
  'RDCOMClient' 'rcom'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
PPT.AddBlankSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'write.table'
PPT.AddDataFrame: no visible global function definition for 'write.csv'
PPT.AddGraphicstoSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.cur'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.list'
PPT.AddGraphicstoSlide: no visible global function definition for
  'savePlot'
PPT.AddTextSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleOnlySlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleSlide: no visible global function definition for
  'comIsValidHandle'
PPT.ApplyTemplate: no visible global function definition for
  'comIsValidHandle'
PPT.Close: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'comCreateObject'
PPT.Init: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'COMCreate'
PPT.Present: no visible global function definition for
  'comIsValidHandle'
PPT.SaveAs: no visible global function definition for
  'comIsValidHandle'
PPT.getAbsolutePath : PPT.filePath: no visible global function
  definition for 'readWindowsShortcut'
Undefined global functions or variables:
  COMCreate comCreateObject comIsValidHandle dev.cur dev.list
  readWindowsShortcut savePlot write.csv write.table
Consider adding
  importFrom("grDevices", "dev.cur", "dev.list", "savePlot")
  importFrom("utils", "write.csv", "write.table")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/race.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rags2ridges)
  > 
  > test_check("rags2ridges")
  -- 1. Failure: armaRidgeP.fused agrees with the old R implmentation (@test-armaR
  isTRUE(...) isn't true.
  
  == testthat results  ===========================================================
  OK: 3893 SKIPPED: 0 FAILED: 1
  1. Failure: armaRidgeP.fused agrees with the old R implmentation (@test-armaRidgeP.fused.R#149) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rags2ridges)
  > 
  > test_check("rags2ridges")
  -- 1. Failure: armaRidgeP.fused agrees with the old R implmentation (@test-armaR
  isTRUE(...) isn't true.
  
  == testthat results  ===========================================================
  OK: 3893 SKIPPED: 0 FAILED: 1
  1. Failure: armaRidgeP.fused agrees with the old R implmentation (@test-armaRidgeP.fused.R#149) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   8.9Mb
Found the following significant warnings:
  Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
See 'd:/Rcompile/CRANpkg/local/3.6/RAMClustR.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.2Mb
    libs   3.0Mb
.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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/randstr.Rcheck/00install.out' for details.
Found the following significant warnings:
  congruRand.c:180:3: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
  congruRand.c:187:2: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
  congruRand.c:188:2: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
  congruRand.c:189:2: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/3.6/randtoolbox.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   2.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs   2.3Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    etc    1.9Mb
    po     1.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.7Mb
Error(s) in re-building vignettes:
--- re-building 'PoS_codata.Rmd' using rmarkdown
--- finished re-building 'PoS_codata.Rmd'

--- re-building 'PoS_interim.Rmd' using rmarkdown
--- finished re-building 'PoS_interim.Rmd'

--- re-building 'customizing_plots.Rmd' using rmarkdown
Loading required package: Rcpp
This is RBesT version 1.3.7
This is bayesplot version 1.6.0
- Online documentation and vignettes at mc-stan.org/bayesplot
- bayesplot theme set to bayesplot::theme_default()
   * Does _not_ affect other ggplot2 plots
   * See ?bayesplot_theme_set for details on theme setting
Final MCMC sample equivalent to less than 1000 independent draws.
Please consider increasing the MCMC simulation size.
--- finished re-building 'customizing_plots.Rmd'

--- re-building 'introduction.Rmd' using rmarkdown
--- finished re-building 'introduction.Rmd'

--- re-building 'introduction_normal.Rmd' using rmarkdown
--- finished re-building 'introduction_normal.Rmd'

--- re-building 'robustMAP.Rmd' using rmarkdown
--- finished re-building 'robustMAP.Rmd'

--- re-building 'variances_MAP.Rmd' using rmarkdown
Quitting from lines 137-148 (variances_MAP.Rmd) 
Error: processing vignette 'variances_MAP.Rmd' failed with diagnostics:
dims [product 2] do not match the length of object [3]
--- failed re-building 'variances_MAP.Rmd'

SUMMARY: processing the following file failed:
  'variances_MAP.Rmd'

Error: Vignette re-building failed.
Execution halted
Running examples in 'rbtc-Ex.R' failed
The error most likely occurred in:

> ### Name: Wif2PrivKey
> ### Title: Create private key from WIF
> ### Aliases: Wif2PrivKey
> 
> ### ** Examples
> 
> pk1 <- createPrivateKey()
Warning in createPrivateKey() :
  
For exemplary purposes, only.
Use at your own risk!

> wif <- PrivKey2Wif(pk1)
Warning in PrivKey2Wif(pk1) :
  
For exemplary purposes, only.
Use at your own risk!

Warning in base58CheckEncode(privkeyextcs) :
  out-of-range values treated as 0 in coercion to raw
> pk2 <- Wif2PrivKey(wif)
Warning in Wif2PrivKey(wif) :
  
For exemplary purposes, only.
Use at your own risk!

Error in Wif2PrivKey(wif) : First character in WIF does neither
correspond to mainnet nor testnet.
Execution halted
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    cont  23.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.0Mb
    po    2.1Mb
Running examples in 'rcongresso-Ex.R' failed
The error most likely occurred in:

> ### Name: fetch_despesas_deputado
> ### Title: Fetches expenditures from deputy
> ### Aliases: fetch_despesas_deputado
> 
> ### ** Examples
> 
> gastos_abel_mesquita <- fetch_despesas_deputado(id = 178957)
Error: Falha na requisicao a API dos Dados Abertos. Erro 400 ao tentar acessar: https://dadosabertos.camara.leg.br/api/v2/deputados/178957/despesas?id=178957
Execution halted
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rcongresso)
  > 
  > test_check("rcongresso")
  -- 1. Error: (unknown) (@test_deputados.R#81)  ---------------------------------
  argument "message" is missing, with no default
  1: skip() at testthat/test_deputados.R:81
  2: structure(list(message = message), class = c("skip", "condition"))
  
  -- 2. Error: (unknown) (@test_proposicoes.R#91)  -------------------------------
  could not find function "FUN1"
  1: check_api() at testthat/test_proposicoes.R:91
  2: tryCatch(setup(), error = function(e) {
         message(e)
         return(FALSE)
     }) at testthat/test_proposicoes.R:15
  3: tryCatchList(expr, classes, parentenv, handlers)
  4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5: value[[3L]](cond)
  6: message(e) at testthat/test_proposicoes.R:16
  7: withRestarts({
         signalCondition(cond)
         defaultHandler(cond)
     }, muffleMessage = function() NULL)
  8: withOneRestart(expr, restarts[[1L]])
  9: doWithOneRestart(return(expr), restart)
  
  -- 3. Error: (unknown) (@test_votacoes.R#70)  ----------------------------------
  argument "message" is missing, with no default
  1: skip() at testthat/test_votacoes.R:70
  2: structure(list(message = message), class = c("skip", "condition"))
  
  == testthat results  ===========================================================
  OK: 13 SKIPPED: 0 FAILED: 3
  1. Error: (unknown) (@test_deputados.R#81) 
  2. Error: (unknown) (@test_proposicoes.R#91) 
  3. Error: (unknown) (@test_votacoes.R#70) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'introducao-rcongresso.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

Quitting from lines 36-38 (introducao-rcongresso.Rmd) 
Error: processing vignette 'introducao-rcongresso.Rmd' failed with diagnostics:
could not find function "FUN1"
--- failed re-building 'introducao-rcongresso.Rmd'

--- re-building 'utilizando-fetch-proposicao.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

Quitting from lines 57-63 (utilizando-fetch-proposicao.Rmd) 
Error: processing vignette 'utilizando-fetch-proposicao.Rmd' failed with diagnostics:
could not find function "FUN1"
--- failed re-building 'utilizando-fetch-proposicao.Rmd'

SUMMARY: processing the following files failed:
  'introducao-rcongresso.Rmd' 'utilizando-fetch-proposicao.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    corpora   7.4Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    include   5.7Mb
    libs      1.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
    libs      1.8Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    include   1.6Mb
    lib       3.9Mb
    libs      2.8Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      1.7Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    include   1.8Mb
    lib       8.9Mb
    libs      1.0Mb
installed size is 35.0Mb
  sub-directories of 1Mb or more:
    include   8.8Mb
    libs     26.1Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    include   6.3Mb
    libs      2.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Running 'testthat.R' [35s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("rdefra")
  > 
  > test_check("rdefra")
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  -- 1. Failure: Metadata should be in the right format (@test-data.R#44)  -------
  `x` not equal to `expected`.
  1 element mismatch
  
  Error in file(file, "rt") : cannot open the connection
  -- 2. Failure: Data should be in the right format (@test-data.R#55)  -----------
  `x` not equal to `expected`.
  'is.NA' value mismatch: 0 in current 1 in target
  
  == testthat results  ===========================================================
  OK: 39 SKIPPED: 1 FAILED: 2
  1. Failure: Metadata should be in the right format (@test-data.R#44) 
  2. Failure: Data should be in the right format (@test-data.R#55) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'rdefra_vignette.Rmd' using knitr
Warning in file(file, "rt") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine sichere in eine nicht sichere Verbindung.'
No data available for station MY1
Warning: Unknown or uninitialised column: 'unit'.
Warning: Unknown or uninitialised column: 'unit'.

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Warning: Unknown or uninitialised column: 'datetime'.
Quitting from lines 117-123 (rdefra_vignette.Rmd) 
Error: processing vignette 'rdefra_vignette.Rmd' failed with diagnostics:
do not know how to convert 'df$datetime' to class "POSIXlt"
--- failed re-building 'rdefra_vignette.Rmd'

SUMMARY: processing the following file failed:
  'rdefra_vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R' [16s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rdhs)
  > 
  > Sys.setenv("rdhs_RENVIRON_PERMISSION" = 1)
  > test_check("rdhs")
  -- 1. Error: update_rdhs_config (@test_miscellaneous.R#97)  --------------------
  cannot open the connection
  1: dhs_data_updates() at testthat/test_miscellaneous.R:97
  2: handle_api_request(endpoint, query, all_results, client, force)
  3: check_for_client()
  4: rdhs_setup()
  5: client_dhs(config = config, root = config$cache_path)
  6: R6_client_dhs$new(config, api_key, root)
  7: .subset2(public_bind_env, "initialize")(...)
  8: saveRDS(self, file.path(root, client_file_name()))
  9: gzfile(file, mode)
  
  trying URL 'https://dhsprogram.com/customcf/legacy/data/sample_download_dataset.cfm?Filename=ZZMR61FL.ZIP&Tp=1&Ctry_Code=zz&survey_id=0&doctype=dhs'
  Content type 'application/x-zip-compressed' length 597481 bytes (583 KB)
  ==================================================
  downloaded 583 KB
  
    adding: temp/RtmpsrcM2S/file334283723401f/ZZMR61FL.DAT (deflated 85%)
  trying URL 'https://dhsprogram.com/customcf/legacy/data/sample_download_dataset.cfm?Filename=ZZAR61FL.ZIP&Tp=4&Ctry_Code=zz&survey_id=0&doctype=hiv'
  Content type 'application/x-zip-compressed' length 81939 bytes (80 KB)
  ==================================================
  downloaded 80 KB
  
  == testthat results  ===========================================================
  OK: 31 SKIPPED: 42 FAILED: 1
  1. Error: update_rdhs_config (@test_miscellaneous.R#97) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  skein_block64.c:226:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.6/RDieHarder.Rcheck/00install.out' for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   2.6Mb
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.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(reinforcelearn)
  > 
  > test_check("reinforcelearn")
  -- 1. Failure: getReplayMemory returns list (@test_accessor_functions.R#22)  ---
  getReplayMemory(agent) not equal to list(...).
  Component 1: Component 2: Mean absolute difference: 1
  Component 1: Component 4: Mean relative difference: 0.03333333
  Component 2: Component 1: Mean relative difference: 0.03333333
  Component 2: Component 4: Mean relative difference: 0.05
  
  == testthat results  ===========================================================
  OK: 20 SKIPPED: 0 FAILED: 1
  1. Failure: getReplayMemory returns list (@test_accessor_functions.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
Package which this enhances but not available for checking: 'Rcplex'
CA: no visible global function definition for 'readClipboard'
LL: no visible global function definition for 'readClipboard'
US: no visible global function definition for 'readClipboard'
delete: no visible global function definition for 'menu'
doc_temp: no visible global function definition for 'menu'
html5: no visible global function definition for 'na.omit'
install_pandoc: no visible global function definition for
  'download.file'
latexlist: no visible global function definition for 'readClipboard'
new_report: no visible global function definition for 'tail'
new_report: no visible global function definition for 'head'
new_report: no visible global function definition for 'menu'
presentation: no visible global function definition for 'head'
presentation: no visible global function definition for 'tail'
presentation: no visible global function definition for 'menu'
repo2github: no visible global function definition for 'download.file'
repo2github: no visible global function definition for 'unzip'
reveal.js: no visible global function definition for 'na.omit'
strWrap: no visible global function definition for 'readClipboard'
update_bib: no visible global function definition for 'tail'
update_bib: no visible global function definition for 'menu'
Undefined global functions or variables:
  download.file head menu na.omit readClipboard tail unzip
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "download.file", "head", "menu", "readClipboard",
             "tail", "unzip")
to your NAMESPACE file.
Running 'restfulr_unit_tests.R' [24s]
Running the tests in 'tests/restfulr_unit_tests.R' failed.
Complete output:
  > require("restfulr") || stop("unable to load restfulr package")
  Loading required package: restfulr
  [1] TRUE
  > restfulr:::.test()
  Loading required namespace: rsolr
  Starting Solr...
  Use options(verbose=TRUE) to diagnose any problems.
  Solr started at: http://localhost:8983/solr/techproducts
  Starting Solr...
  Use options(verbose=TRUE) to diagnose any problems.
  Solr started at: http://localhost:8983/solr/techproducts
  Timing stopped at: 0.07 0.12 4.46
  Error in function (type, msg, asError = TRUE)  : 
    Failed to connect to localhost port 8983: Connection refused
  Starting Solr...
  Use options(verbose=TRUE) to diagnose any problems.
  Solr started at: http://localhost:8983/solr/techproducts
  Timing stopped at: 0.07 0.16 3.57
  Error : Service Unavailable
  
  
  
  RUNIT TEST PROTOCOL -- Tue Mar 05 06:11:36 2019 
  *********************************************** 
  Number of test functions: 3 
  Number of errors: 2 
  Number of failures: 0 
  
   
  1 Test Suite : 
  restfulr RUnit Tests - 3 test functions, 2 errors, 0 failures
  ERROR in test_RestContainer_CRUD: Error in function (type, msg, asError = TRUE)  : 
    Failed to connect to localhost port 8983: Connection refused
  ERROR in test_RestUri_CRUD: Error : Service Unavailable
  
  
  Test files with failing tests
  
     test_RestContainer.R 
       test_RestContainer_CRUD 
  
     test_RestUri.R 
       test_RestUri_CRUD 
  
  
  Error in testPackage("restfulr") : unit tests failed for package restfulr
  Calls: <Anonymous> -> testPackage
  Configuration is not valid, terminating server
  Execution halted
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
installed size is 80.3Mb
  sub-directories of 1Mb or more:
    gdal       3.9Mb
    libs      68.7Mb
    pictures   1.3Mb
    proj       5.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.8Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    fonts   1.5Mb
    libs    2.0Mb
Packages suggested but not available for checking: 'pmg', 'SVGAnnotation'
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extra   9.3Mb
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.7Mb
    libs   5.1Mb
File 'RGtk2/libs/i386/RGtk2.dll':
  Found non-API calls to R: 'R_new_custom_connection',
    'Rf_EncodeInteger', 'Rf_EncodeLogical', 'Rf_EncodeReal',
    'Rf_formatInteger', 'Rf_formatLogical', 'Rf_formatReal'
File 'RGtk2/libs/x64/RGtk2.dll':
  Found non-API calls to R: 'R_new_custom_connection',
    'Rf_EncodeInteger', 'Rf_EncodeLogical', 'Rf_EncodeReal',
    'Rf_formatInteger', 'Rf_formatLogical', 'Rf_formatReal'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-1'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 40-46 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
package or namespace load failed for 'ggtree':
 object 'as_data_frame' is not exported by 'namespace:tidytree'
--- failed re-building 'introduction.Rmd'

SUMMARY: processing the following file failed:
  'introduction.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    lib    3.5Mb
    libs   4.8Mb
File 'RInside/libs/i386/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/i386/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  jri.h:21:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri.c:308:27: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri_glue.c:24:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.6/rJava.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.6/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.6/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Mallows: no visible global function definition for 'runif'
Mallows: no visible global function definition for 'x11'
Mallows: no visible global function definition for 'plot'
Mallows: no visible global function definition for 'dev.off'
UpdateLambda: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  dev.off plot runif uniroot x11
Consider adding
  importFrom("grDevices", "dev.off", "x11")
  importFrom("graphics", "plot")
  importFrom("stats", "runif", "uniroot")
to your NAMESPACE file.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    rmd   8.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   2.1Mb
Running examples in 'rms-Ex.R' failed
The error most likely occurred in:

> ### Name: Function
> ### Title: Compose an S Function to Compute X beta from a Fit
> ### Aliases: Function.rms Function.cph sascode perlcode
> ### Keywords: regression methods interface models survival math
> 
> ### ** Examples
> 
> set.seed(1331)
> x1 <- exp(rnorm(100))
> x2 <- factor(sample(c('a','b'),100,rep=TRUE))
> dd <- datadist(x1, x2)
> options(datadist='dd')
> y  <- log(x1)^2+log(x1)*(x2=='b')+rnorm(100)/4
> f  <- ols(y ~ pol(log(x1),2)*x2)
> f$coef
   Intercept           x1         x1^2         x2=b    x1 * x2=b  x1^2 * x2=b 
-0.001885864 -0.019198566  1.017432226  0.047810769  1.037259829 -0.032005994 
> g  <- Function(f, digits=5)
> g
function (x1 = 1.0906, x2 = "b") 
{
    x1 <- log(x1)
    -0.0018859 - 0.019199 * x1 + 1.0174 * x1^2 + 0.047811 * (x2 == 
        "b") + (x2 == "b") * (1.0373 * x1 - 0.032006 * x1^2)
}
<environment: 0x087e35d8>
> sascode(g)
    x1 = log(x1)
    -0.0018859 - 0.019199 * x1 + 1.0174 * x1**2 + 0.047811 * (x2 = 
        "b") + (x2 = "b") * (1.0373 * x1 - 0.032006 * x1**2);
> cat(perlcode(g), '\n')
Error in expr[[3]] : subscript out of bounds
Calls: cat ... convert -> f -> paste -> convert -> f -> paste -> convert
Execution halted
Running examples in 'rms-Ex.R' failed
The error most likely occurred in:

> ### Name: Function
> ### Title: Compose an S Function to Compute X beta from a Fit
> ### Aliases: Function.rms Function.cph sascode perlcode
> ### Keywords: regression methods interface models survival math
> 
> ### ** Examples
> 
> set.seed(1331)
> x1 <- exp(rnorm(100))
> x2 <- factor(sample(c('a','b'),100,rep=TRUE))
> dd <- datadist(x1, x2)
> options(datadist='dd')
> y  <- log(x1)^2+log(x1)*(x2=='b')+rnorm(100)/4
> f  <- ols(y ~ pol(log(x1),2)*x2)
> f$coef
   Intercept           x1         x1^2         x2=b    x1 * x2=b  x1^2 * x2=b 
-0.001885864 -0.019198566  1.017432226  0.047810769  1.037259829 -0.032005994 
> g  <- Function(f, digits=5)
> g
function (x1 = 1.0906, x2 = "b") 
{
    x1 <- log(x1)
    -0.0018859 - 0.019199 * x1 + 1.0174 * x1^2 + 0.047811 * (x2 == 
        "b") + (x2 == "b") * (1.0373 * x1 - 0.032006 * x1^2)
}
<environment: 0x000000001144ad18>
> sascode(g)
    x1 = log(x1)
    -0.0018859 - 0.019199 * x1 + 1.0174 * x1**2 + 0.047811 * (x2 = 
        "b") + (x2 = "b") * (1.0373 * x1 - 0.032006 * x1**2);
> cat(perlcode(g), '\n')
Error in expr[[3]] : subscript out of bounds
Calls: cat ... convert -> f -> paste -> convert -> f -> paste -> convert
Execution halted
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rngtools)
  Loading required package: pkgmaker
  Loading required package: registry
  
  Attaching package: 'pkgmaker'
  
  The following object is masked from 'package:base':
  
      isFALSE
  
  > 
  > test_check("rngtools")
  -- 1. Failure: RNGtype (@test-format.R#100)  -----------------------------------
  length(d) not identical to `expL`.
  1/1 mismatches
  [1] 3 - 2 == 1
  MISSING : result has correct length ( [ 2 ) ]
  
  -- 2. Failure: RNGtype (@test-format.R#101)  -----------------------------------
  length(d) not identical to `expL`.
  1/1 mismatches
  [1] 3 - 2 == 1
  numeric(1) : result has correct length ( [ 2 ) Valid single numeric seed ]
  
  -- 3. Failure: RNGtype (@test-format.R#102)  -----------------------------------
  length(d) not identical to `expL`.
  1/1 mismatches
  [1] 3 - 2 == 1
  integer(3) : result has correct length ( [ 2 ) Valid seed ]
  
  -- 4. Failure: RNGtype (@test-format.R#103)  -----------------------------------
  length(d) not identical to `expL`.
  1/1 mismatches
  [1] 3 - 2 == 1
  integer(1) : result has correct length ( [ 2 ) Valid encoded kind ]
  
  -- 5. Failure: RNGtype (@test-format.R#106)  -----------------------------------
  length(d) not identical to `expL`.
  1/1 mismatches
  [1] 3 - 2 == 1
  list(2) : result has correct length ( [ 2 ) list with rng slot ]
  
  == testthat results  ===========================================================
  OK: 225 SKIPPED: 0 FAILED: 5
  1. Failure: RNGtype (@test-format.R#100) 
  2. Failure: RNGtype (@test-format.R#101) 
  3. Failure: RNGtype (@test-format.R#102) 
  4. Failure: RNGtype (@test-format.R#103) 
  5. Failure: RNGtype (@test-format.R#106) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      5.5Mb
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rnn)
  > 
  > test_check("rnn")
  -- 1. Failure: (unknown) (@test_rnn.R#66)  -------------------------------------
  sum(bin2int(B)) not equal to 888626.
  1/1 mismatches
  [1] 209284 - 888626 == -679342
  
  == testthat results  ===========================================================
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test_rnn.R#66) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
See 'd:/Rcompile/CRANpkg/local/3.6/RobLoxBioC.Rcheck/00install.out' for details.
'LinkingTo' for 'mgcv' is unused as it has no 'include' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.3Mb
    libs   2.2Mb
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rPackedBar)
  > 
  > test_check("rPackedBar")
  -- 1. Failure: object value (@test-gen_gray_bars.R#277)  -----------------------
  `test` not equivalent to `expected`.
  Component "bar_list": Component 1: Component 2: 1 string mismatch
  Component "bar_list": Component 1: Component 3: Component 1: 1 string mismatch
  Component "bar_list": Component 2: Component 2: 1 string mismatch
  Component "bar_list": Component 2: Component 3: Component 1: 1 string mismatch
  Component "bar_list": Component 3: Component 2: 1 string mismatch
  Component "bar_list": Component 3: Component 3: Component 1: 1 string mismatch
  Component "bar_list": Component 4: Component 2: 1 string mismatch
  Component "bar_list": Component 4: Component 3: Component 1: 1 string mismatch
  Component "bar_list": Component 5: Component 2: 1 string mismatch
  ...
  
  == testthat results  ===========================================================
  OK: 43 SKIPPED: 0 FAILED: 1
  1. Failure: object value (@test-gen_gray_bars.R#277) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      2.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.7Mb
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  27.0Mb
Found the following significant warnings:
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.6/Rserve.Rcheck/00install.out' for details.
Rserve: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.6/Rserve/libs/i386/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'd:/Rcompile/CRANpkg/lib/3.6/Rserve/libs/x64/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/i386/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Running 'testthat.R' [46s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("RSSL")
  Loading required package: RSSL
  -- 1. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#53)
  sum(predict(g_sup, problem$X_test) == problem$y_test) not equal to 61.
  1/1 mismatches
  [1] 55 - 61 == -6
  
  -- 2. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#54)
  sum(predict(g_semi, problem$X_test) == problem$y_test) not equal to 61.
  1/1 mismatches
  [1] 55 - 61 == -6
  
  -- 3. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#55)
  sum(predict(g_euc, problem$X_test) == problem$y_test) not equal to 57.
  1/1 mismatches
  [1] 55 - 57 == -2
  
  -- 4. Failure: Multiclass gives an output (@test-LeastSquaresClassifier.R#46)  -
  sum(...) not equal to 61.
  1/1 mismatches
  [1] 60 - 61 == -1
  
  == testthat results  ===========================================================
  OK: 466 SKIPPED: 0 FAILED: 4
  1. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#53) 
  2. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#54) 
  3. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#55) 
  4. Failure: Multiclass gives an output (@test-LeastSquaresClassifier.R#46) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [48s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("RSSL")
  Loading required package: RSSL
  -- 1. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#53)
  sum(predict(g_sup, problem$X_test) == problem$y_test) not equal to 61.
  1/1 mismatches
  [1] 55 - 61 == -6
  
  -- 2. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#54)
  sum(predict(g_semi, problem$X_test) == problem$y_test) not equal to 61.
  1/1 mismatches
  [1] 55 - 61 == -6
  
  -- 3. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#55)
  sum(predict(g_euc, problem$X_test) == problem$y_test) not equal to 57.
  1/1 mismatches
  [1] 55 - 57 == -2
  
  -- 4. Failure: Multiclass gives an output (@test-LeastSquaresClassifier.R#46)  -
  sum(...) not equal to 61.
  1/1 mismatches
  [1] 60 - 61 == -1
  
  == testthat results  ===========================================================
  OK: 466 SKIPPED: 0 FAILED: 4
  1. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#53) 
  2. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#54) 
  3. Failure: Multi class gives an output (@test-ICLeastSquaresClassifier.R#55) 
  4. Failure: Multiclass gives an output (@test-LeastSquaresClassifier.R#46) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  17.4Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    Lib  11.5Mb
Math.Sym: no visible binding for global variable 'transtab'
jythonStart: no visible global function definition for '.jinit'
jythonStart: no visible global function definition for '.jnew'
jythonStart: no visible binding for global variable '.Jython'
sympy: no visible binding for global variable '.Jython'
sympy: no visible global function definition for '.jstrVal'
sympyStart: no visible binding for global variable '.Jython'
Undefined global functions or variables:
  .Jython .jinit .jnew .jstrVal transtab
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Running 'test-all.R' [38s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("rtext")
  Loading required package: rtext
  Loading required package: stringb
  -- 1. Error: rtext tokenize_data_words (@test_rtext.R#98)  ---------------------
  arguments must have same length
  1: expect_true({
         dings <- rtext$new("meine mudder schneidet speck - ho-narroh")
         dings$char_data_set("test", 1:5, 1)
         dings$char_data_set("toast", 1:dings$char_length(), "uggah")
         dings$char_data_get()
         length(dings$tokenize_data_words()$test) == 6
     }) at testthat/test_rtext.R:98
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: dings$tokenize_data_words() at testthat/test_rtext.R:103
  5: self$tokenize_data_regex(split = split, ignore.case = ignore.case, fixed = fixed, 
         perl = perl, useBytes = useBytes, non_token = non_token, join = join, aggregate_function = aggregate_function, 
         ...)
  6: self$tokenize_data_sequences(token = token, join = join, aggregate_function = aggregate_function, 
         ...)
  7: stats::aggregate(chardata[, -c(1:2)], by = list(token_i = token_i), FUN = "modus", 
         multimodal = NA, warn = FALSE)
  8: aggregate.data.frame(chardata[, -c(1:2)], by = list(token_i = token_i), FUN = "modus", 
         multimodal = NA, warn = FALSE)
  9: stop("arguments must have same length")
  
  == testthat results  ===========================================================
  OK: 281 SKIPPED: 0 FAILED: 1
  1. Error: rtext tokenize_data_words (@test_rtext.R#98) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.8Mb
    projects   2.7Mb
Running examples in 'rtson-Ex.R' failed
The error most likely occurred in:

> ### Name: readTSON
> ### Title: Deserialize a connection
> ### Aliases: readTSON
> 
> ### ** Examples
> 
> ## Example
> 
> library(rtson)
> 
> list = list(integer=42L,
+             double=42,
+             bool=TRUE,
+             uint8=tson.uint8.vec(c(42,0)),
+             uint16=tson.uint16.vec(c(42,0)),
+             uint32=tson.uint32.vec(c(42,0)),
+             int8=tson.int8.vec(c(42,0)),
+             int16=tson.int16.vec(c(42,0)),
+             int32=as.integer(c(42,0)),
+             float32=tson.float32.vec(c(0.0, 42.0)),
+             float64=c(42.0,42.0),
+             map=list(x=42, y=42, label="42"),
+             list=list("42",42)
+ )
> 
> con = rawConnection(raw(0), "r+")
> writeTSON(list, con)
<Serializer>
  Public:
    addBool: function (object) 
    addDouble: function (object) 
    addDoubleList: function (object) 
    addFloat32List: function (object) 
    addFloat64List: function (object) 
    addInt16List: function (object) 
    addInt32List: function (object) 
    addInt8List: function (object) 
    addInteger: function (object) 
    addIntegerList: function (object) 
    addLength: function (len) 
    addList: function (object) 
    addListOrMap: function (object) 
    addMap: function (object) 
    addNull: function () 
    addObject: function (object) 
    addRootObject: function (object) 
    addString: function (object) 
    addStringList: function (object) 
    addType: function (type) 
    addUInt16List: function (object) 
    addUInt32List: function (object) 
    addUInt8List: function (object) 
    clone: function (deep = FALSE) 
    con: 3
    initialize: function (object, con) 
> bytes = rawConnectionValue(con)
> close(con)
> con = rawConnection(bytes, "r")
> object = readTSON(con)
> 
> 
> 
> cleanEx()
Error: connections left open:
	bytes (rawConnection)
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   2.2Mb
Package suggested but not available for checking: 'gpuR'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    include   5.2Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    include   2.5Mb
    libs      8.1Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
File 'RWinEdt/R/zzz.R':
  .onAttach calls:
    writeLines(edtFile, con = send2RedtLoc)
    writeLines(edtFile, con = send2RedtLoc)

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
Package suggested but not available for checking: 'SnakeCharmR'
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   5.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    sample_data   3.0Mb
Found the following significant warnings:
  d:/Compiler/gcc-4.9.3/local330/include/gmp-x64.h:140:23: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/Compiler/gcc-4.9.3/local330/include/gmp-x64.h:141:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.6/sbrl.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.
Running examples in 'scorecardModelUtils-Ex.R' failed
The error most likely occurred in:

> ### Name: scalling
> ### Title: Converting coefficients of logistic regression into scores for
> ###   scorecard building
> ### Aliases: scalling
> 
> ### ** Examples
> 
> data <- iris
> set.seed(11)
> data$Y <- sample(0:1,size=nrow(data),replace=TRUE)
> x <- c("Sepal.Length","Sepal.Width","Petal.Length","Petal.Width")
> iv_table_list <- iv_table(base = data,target = "Y",num_var_name = x,cat_var_name = "Species")
> num_cat <- num_to_cat(base = data,num_woe_table = iv_table_list$num_woe_table)
> log_model <- glm(Y ~ ., data = num_cat, family = "binomial")
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: glm ... model.matrix -> model.matrix.default -> contrasts<-
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   3.5Mb
Running examples in 'secret-Ex.R' failed
The error most likely occurred in:

> ### Name: add_github_user
> ### Title: Add a user via their GitHub username.
> ### Aliases: add_github_user
> 
> ### ** Examples
> 
> vault <- file.path(tempdir(), ".vault")
> create_vault(vault)
> 
> add_github_user("hadley", vault = vault)
> list_users(vault = vault)
[1] "github-hadley"
> delete_user("github-hadley", vault = vault)
> 
> 
> 
> cleanEx()
Error: connections left open:
	file (textConnection)
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.5Mb
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("sentimentr")
  > 
  > test_check("sentimentr")
  -- 1. Failure: extract_sentiment_terms extracts the terms (@test-extract_sentime
  pol_words$negative[1:3] not equal to list(character(0), c("wait", "restless", "fire"), character(0)).
  Component 2: Lengths (0, 3) differ (string compare on first 0)
  
  == testthat results  ===========================================================
  OK: 32 SKIPPED: 0 FAILED: 1
  1. Failure: extract_sentiment_terms extracts the terms (@test-extract_sentiment_terms.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   3.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Error(s) in re-building vignettes:
--- re-building 'Introduction.Rmd' using rmarkdown
trying URL 'https://pure.strath.ac.uk/portal/files/43595106/Figure_2.zip'
Quitting from lines 38-41 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
cannot open URL 'https://pure.strath.ac.uk/portal/files/43595106/Figure_2.zip'
--- failed re-building 'Introduction.Rmd'

SUMMARY: processing the following file failed:
  'Introduction.Rmd'

Error: Vignette re-building failed.
Execution halted
capture: no visible binding for global variable 'resultText'
restore.session: no visible binding for global variable
  '.save.session.packages'
restore.session: no visible binding for global variable
  '.save.session.search'
save.session: no visible global function definition for 'dev.list'
save.session: no visible binding for '<<-' assignment to
  '.save.session.search'
save.session: no visible binding for '<<-' assignment to
  '.save.session.packages'
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.
installed size is 94.0Mb
  sub-directories of 1Mb or more:
    doc     11.2Mb
    gdal     3.9Mb
    libs    70.0Mb
    proj     5.0Mb
    sqlite   1.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    www   7.3Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    www   7.8Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sigmajs)
  Welcome to sigmajs
  
  Docs: sigmajs.john-coene.com
  > 
  > test_check("sigmajs")
  Found # 4 clusters
  -- 1. Failure: delay (@test-graph.R#50)  ---------------------------------------
  unlist(unname(sg$x$addNodesDelay[[1]][5])) not equal to " 566.004".
  1/1 mismatches
  x[1]: " 548.9736"
  y[1]: " 566.004"
  
  == testthat results  ===========================================================
  OK: 65 SKIPPED: 0 FAILED: 1
  1. Failure: delay (@test-graph.R#50) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(simcdm)
  > 
  > test_check("simcdm")
  -- 1. Failure: Simulation of attributes matches (@test-attributes.R#71)  -------
  `subject_alphas_func` not equal to `subject_alphas_base`.
  34/60 mismatches (average diff: 1)
  [1]  0 - 1 == -1
  [3]  0 - 1 == -1
  [4]  1 - 0 ==  1
  [5]  1 - 0 ==  1
  [6]  0 - 1 == -1
  [10] 1 - 0 ==  1
  [12] 0 - 1 == -1
  [14] 0 - 1 == -1
  [15] 1 - 0 ==  1
  ...
  Equivalent subject alpha Generation
  
  == testthat results  ===========================================================
  OK: 14 SKIPPED: 0 FAILED: 1
  1. Failure: Simulation of attributes matches (@test-attributes.R#71) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.9Mb
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SimplifyStats)
  > 
  > test_check("SimplifyStats")
  
  The Shapiro-Wilk test requires 3 < N < 5000.
  
  -- 1. Failure: valid input produce valid output (@test.group_summarize.R#34)  --
  {
      ...
  } isn't true.
  
  == testthat results  ===========================================================
  OK: 8 SKIPPED: 0 FAILED: 1
  1. Failure: valid input produce valid output (@test.group_summarize.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   2.5Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tthread/tinythread.h:632:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tbb/tbb_stddef.h:470:37: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tbb/atomic.h:29:30: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tbb/tick_count.h:42:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tbb/tick_count.h:43:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tbb/tick_count.h:75:21: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tbb/tick_count.h:102:10: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tbb/tick_count.h:80:37: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tbb/tick_count.h:127:30: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.6/skm.Rcheck/00install.out' for details.
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(slouch)
  > 
  > # testsetup <- function(){
  > #   pars <- list(myfunc = myfunc, dummydata = dummydata, model.id.btk = model.id.btk)
  > #   return(pars)
  > # }
  > 
  > test_check("slouch")
  -- 1. Failure: No errors ANOVA (@test_anova.R#37)  -----------------------------
  structure(...) not equal to m1$beta_primary$coefficients.
  3/4 mismatches (average diff: 0.0444)
  [1] 0.4216 - 0.4893 == -0.06774
  [2] 0.4815 - 0.4220 ==  0.05951
  [4] 0.0504 - 0.0445 ==  0.00591
  
  == testthat results  ===========================================================
  OK: 9 SKIPPED: 0 FAILED: 1
  1. Failure: No errors ANOVA (@test_anova.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SmartEDA)
  > 
  > 
  > context("Summary statistics")
  > 
  > test_that("ExpKurtosis and ExpSkew are measures of shapes value", {
  +   expect_equal(ExpKurtosis(c(1:4),type="moment"), 1.64)
  +   set.seed(1234)
  +   expect_equal(ExpSkew(sample(1:100,10),type="moment"),-0.2131082)
  + })
  Error: Test failed: 'ExpKurtosis and ExpSkew are measures of shapes value'
  * ExpSkew(sample(1:100, 10), type = "moment") not equal to -0.2131082.
  1/1 mismatches
  [1] 0.618 - -0.213 == 0.831
  Execution halted
Running 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # setting R_TESTS to empty string because of
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # revert this when that issue in R is fixed.
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(Smisc)
  > 
  > # There shouldn't be any files in the tmp folder
  > unlink("testthat/tmp", recursive = TRUE, force = TRUE)
  > dir.create("testthat/tmp")
  > 
  > test_check("Smisc")
  -- 1. Failure: parseJob() doesn't deviate from historical behavior (@test_parseJ
  `xout` not equal to `xin`.
  Component "x2": Component 1: Mean relative difference: 0.8461538
  Component "x2": Component 2: Mean relative difference: 0.7532468
  Component "x2": Component 3: Mean relative difference: 0.5416667
  Component "x2": Component 4: Mean relative difference: 0.34375
  Component "x2": Component 5: Mean relative difference: 0.5441176
  
  == testthat results  ===========================================================
  OK: 286 SKIPPED: 0 FAILED: 1
  1. Failure: parseJob() doesn't deviate from historical behavior (@test_parseJob.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.4Mb
Running examples in 'SNPknock-Ex.R' failed
The error most likely occurred in:

> ### Name: SNPknock.fp.loadFit
> ### Title: Load the parameter estimates obtained by fastPHASE
> ### Aliases: SNPknock.fp.loadFit
> 
> ### ** Examples
> 
> # Specify the location of the fastPHASE output files containing the parameter estimates.
> # Example files can be found in the package installation directory.
> r_file = system.file("extdata", "genotypes_rhat.txt", package = "SNPknock")
> alpha_file = system.file("extdata", "genotypes_alphahat.txt", package = "SNPknock")
> theta_file = system.file("extdata", "genotypes_thetahat.txt", package = "SNPknock")
> char_file = system.file("extdata", "genotypes_origchars", package = "SNPknock")
> 
> # Read the parameter files and build the HMM
> hmm = SNPknock.fp.loadFit(r_file, alpha_file, theta_file, char_file)
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	lines (textConnection)
	lines (textConnection)
	lines (textConnection)
	lines (textConnection)
Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("SOMbrero")
  Loading required package: igraph
  
  Attaching package: 'igraph'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  The following objects are masked from 'package:stats':
  
      decompose, spectrum
  
  The following object is masked from 'package:base':
  
      union
  
  
  ***********************************************************
  
        This is 'SOMbrero' package, v 1.2
  
  Citation details with citation('SOMbrero')
  
  Further information with help(SOMbrero)...
  
  Use sombreroGUI() to start the Graphical Interface.
  
  ***********************************************************
  > 
  > test_check("SOMbrero")
  -- 1. Failure: case relational - radius 'letremy' and affectation 'heskes' (@tes
  predict(rsom, dissim.lesmis) not equal to rsom$clustering.
  2/77 mismatches (average diff: 6)
  [44] 22 - 16 == 6
  [56] 22 - 16 == 6
  
  -- 2. Failure: case relational - radius 'letremy' and affectation 'heskes' (@tes
  predict(rsom) not equal to rsom$clustering.
  2/77 mismatches (average diff: 6)
  [44] 22 - 16 == 6
  [56] 22 - 16 == 6
  
  == testthat results  ===========================================================
  OK: 26 SKIPPED: 0 FAILED: 2
  1. Failure: case relational - radius 'letremy' and affectation 'heskes' (@test-prediction.R#61) 
  2. Failure: case relational - radius 'letremy' and affectation 'heskes' (@test-prediction.R#63) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   2.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
Running 'test-all.R' [94s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.tools")
  Loading required package: SpaDES.tools
  -- 1. Failure: spread produces legal RasterLayer (@test-spread.R#60)  ----------
  all(...) isn't true.
  
  -- 2. Failure: spreadProb with relative values does not work correctly (@test-sp
  sum(hab3[events1[] > 0]) > sum(hab3[events2[] > 0]) isn't true.
  
  -- 3. Failure: spread2 tests (@test-spread2.R#220)  ----------------------------
  cht$p.value > 0.05 isn't true.
  
  [1] "Scales with number of starts, not maxSize of raster"
  -- 4. Failure: spread2 tests -- asymmetry (@test-spread2.R#710)  ---------------
  circs[sams] == circs[ciCentre[] == 1] isn't true.
  
  == testthat results  ===========================================================
  OK: 1048 SKIPPED: 11 FAILED: 4
  1. Failure: spread produces legal RasterLayer (@test-spread.R#60) 
  2. Failure: spreadProb with relative values does not work correctly (@test-spread.R#1259) 
  3. Failure: spread2 tests (@test-spread2.R#220) 
  4. Failure: spread2 tests -- asymmetry (@test-spread2.R#710) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'test-all.R' [96s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.tools")
  Loading required package: SpaDES.tools
  -- 1. Failure: spread produces legal RasterLayer (@test-spread.R#60)  ----------
  all(...) isn't true.
  
  -- 2. Failure: spreadProb with relative values does not work correctly (@test-sp
  sum(hab3[events1[] > 0]) > sum(hab3[events2[] > 0]) isn't true.
  
  -- 3. Failure: spread2 tests (@test-spread2.R#220)  ----------------------------
  cht$p.value > 0.05 isn't true.
  
  [1] "Scales with number of starts, not maxSize of raster"
  -- 4. Failure: spread2 tests -- asymmetry (@test-spread2.R#710)  ---------------
  circs[sams] == circs[ciCentre[] == 1] isn't true.
  
  == testthat results  ===========================================================
  OK: 1048 SKIPPED: 11 FAILED: 4
  1. Failure: spread produces legal RasterLayer (@test-spread.R#60) 
  2. Failure: spreadProb with relative values does not work correctly (@test-spread.R#1259) 
  3. Failure: spread2 tests (@test-spread2.R#220) 
  4. Failure: spread2 tests -- asymmetry (@test-spread2.R#710) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'spa-Ex.R' failed
The error most likely occurred in:

> ### Name: predict.spa
> ### Title: Inductive Predict Procedure For SPA
> ### Aliases: predict.spa
> ### Keywords: classes models methods
> 
> ### ** Examples
> 
> ## Use simulated example (two moon) and generate a contour plot of the border
> set.seed(100)
> dat=spa.sim(type="moon") 
> 
> L=which(!is.na(dat$y))
> U=which(is.na(dat$y))
> Dij=as.matrix(daisy(dat[,-1]))
> 
> ##Use spa to train with a supervised/transductive kernel smoother
> gsup<-spa(dat$y[L],graph=Dij[L,L],control=spa.control(gcv="lGCV"))
Error in if (g1 < g2) { : missing value where TRUE/FALSE needed
Calls: spa -> spa.gcv
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.7Mb
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    R      5.1Mb
    doc    4.8Mb
    help   5.1Mb
    libs   1.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Output for data("spinalCord", package = "specmine"):
  Warning messages:
  1: In fun(libname, pkgname) :
    mzR has been built against a different Rcpp version (0.12.17)
  than is installed on your system (1.0.0). This might lead to errors
  when loading mzR. If you encounter such issues, please send a report,
  including the output of sessionInfo() to the Bioc support forum at 
  https://support.bioconductor.org/. For details see also
  https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
  2: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
    package instead.
Running 'testthat.R' [23s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spew)
  > 
  > test_check("spew")
  -- 1. Error: Moment Matching (@test-sampling.R#32)  ----------------------------
  abs(2.8 - mean(pums[inds, ]$NP)) < 0.05 is not TRUE
  1: stopifnot(abs(2.8 - mean(pums[inds, ]$NP)) < 0.05) at testthat/test-sampling.R:32
  
  [1] "Place has 0 Households!"
  == testthat results  ===========================================================
  OK: 101 SKIPPED: 7 FAILED: 1
  1. Error: Moment Matching (@test-sampling.R#32) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(splitstackshape)
  > 
  > test_check("splitstackshape")
  -- 1. Failure: stratified returns the expected number of rows (@test_stratified.
  nrow(stratified(DF, "A", 0.1, select = list(A = c("AA", "BB")))) not equal to 3.
  1/1 mismatches
  [1] 4 - 3 == 1
  
  == testthat results  ===========================================================
  OK: 51 SKIPPED: 0 FAILED: 1
  1. Failure: stratified returns the expected number of rows (@test_stratified.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.7Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   2.0Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
stkde: no visible global function definition for 'npudensbw'
stkde: no visible global function definition for 'npudens'
stkde: no visible global function definition for 'quantile'
stkde: no visible global function definition for 'heat.colors'
stkde: no visible global function definition for 'par'
stkde: no visible global function definition for 'image'
stkde: no visible global function definition for 'contour'
stkde.base: no visible global function definition for 'npudensbw'
stkde.base: no visible global function definition for 'npudens'
stkde.sig: no visible global function definition for 'SpatialPoints'
stkde.sig: no visible global function definition for 'spsample'
stkde.sig: no visible global function definition for 'bbox'
stkde.sig: no visible global function definition for 'quantile'
stkde.sig: no visible global function definition for 'heat.colors'
stkde.sig: no visible global function definition for 'par'
stkde.sig: no visible global function definition for 'image'
stkde.sig: no visible global function definition for 'contour'
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    include   9.0Mb
Error(s) in re-building vignettes:
--- re-building 'stmVignette.Rnw' using Sweave
stm v1.3.3 (2018-1-26) successfully loaded. See ?stm for help. 
 Papers, resources, and other materials at structuraltopicmodel.com
Warning in load(url("http://goo.gl/VPdxlS")) :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine sichere in eine nicht sichere Verbindung.'

Error: processing vignette 'stmVignette.Rnw' failed with diagnostics:
 chunk 7 
Error in load(url("http://goo.gl/VPdxlS")) : cannot open the connection

--- failed re-building 'stmVignette.Rnw'

SUMMARY: processing the following file failed:
  'stmVignette.Rnw'

Error: Vignette re-building failed.
Execution halted