PharmPow_crossover: no visible global function definition for
  ‘read.table’
PharmPow_crossover: no visible global function definition for
  ‘write.csv’
PharmPow_crossover: no visible global function definition for ‘pdf’
PharmPow_crossover: no visible global function definition for ‘dev.off’
PharmPow_parallel: no visible global function definition for
  ‘read.table’
PharmPow_parallel: no visible global function definition for
  ‘write.csv’
PharmPow_parallel: no visible global function definition for ‘pdf’
PharmPow_parallel: no visible global function definition for ‘dev.off’
fig_PharmPow_crossover: no visible global function definition for
  ‘read.csv’
fig_PharmPow_parallel: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  dev.off pdf read.csv read.table write.csv
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "read.csv", "read.table", "write.csv")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Undeclared package ‘phase1RMD’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.pdf’
fox: no visible binding for global variable ‘sd’
fox: no visible global function definition for ‘cor’
fox: no visible global function definition for ‘interaction.plot’
fox: no visible global function definition for ‘reorder’
kang: no visible global function definition for ‘var’
kang: no visible binding for global variable ‘sd’
kang: no visible global function definition for ‘cor’
kang: no visible global function definition for ‘interaction.plot’
kang: no visible global function definition for ‘reorder’
nahu: no visible global function definition for ‘interaction.plot’
nahu: no visible global function definition for ‘reorder’
thsu: no visible global function definition for ‘median’
thsu: no visible binding for global variable ‘sd’
thsu: no visible global function definition for ‘cor’
thsu: no visible global function definition for ‘interaction.plot’
thsu: no visible global function definition for ‘reorder’
Undefined global functions or variables:
  cor interaction.plot median reorder sd var
Consider adding
  importFrom("stats", "cor", "interaction.plot", "median", "reorder",
             "sd", "var")
to your NAMESPACE file.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
pheno.ddm: no visible global function definition for ‘new’
pheno.flm.fit: no visible binding for global variable ‘na.exclude’
pheno.flm.fit: no visible global function definition for ‘terms’
pheno.flm.fit: no visible global function definition for ‘residuals’
pheno.flm.fit: no visible global function definition for ‘qt’
pheno.lad.fit: no visible binding for global variable ‘na.exclude’
pheno.mlm.fit: no visible binding for global variable ‘na.exclude’
pheno.mlm.fit: no visible global function definition for ‘residuals’
Undefined global functions or variables:
  na.exclude new qt residuals terms
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "na.exclude", "qt", "residuals", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Rd file 'pheno.mlm.fit.Rd':
  \examples lines wider than 100 characters:
             R <- pheno.mlm.fit(DWD)                                                         # parameter estimation
             summary(tr)$coef[2]                                                                     # slope of trend
             summary(tr)$coef[4]                                                                     # standard error of trend

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘vowels’ in Rd xrefs
Found the following files/directories:
  ‘1khz.wav’ ‘snd.wav’
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
Undeclared package ‘photobiologyLEDs’ in Rd xrefs
Note: found 1 marked Latin-1 string
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    help   1.1Mb
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘phylin_tutorial.Snw’ using Sweave

Error: processing vignette 'phylin_tutorial.Snw' failed with diagnostics:
 chunk 22 (label = krigImg) 
Error in tapply(intpl, list(grid[, 1], grid[, 2]), mean) : 
  arguments must have same length

--- failed re-building ‘phylin_tutorial.Snw’

--- re-building ‘resistance_tutorial.Snw’ using Sweave
Loading required package: raster
Loading required package: sp
Loading required package: igraph

Attaching package: ‘igraph’

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

    union

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

    decompose, spectrum

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

    union

Loading required package: Matrix

Attaching package: ‘gdistance’

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

    normalize

Warning in gen.variogram(geo.dist, simul.gen.dist, lag = 0.01) :
  The variogram contains NAs.Consider adjusting the lag.
Warning in gen.variogram(res.dist, simul.gen.dist, lag = 120) :
  The variogram contains NAs.Consider adjusting the lag.

Error: processing vignette 'resistance_tutorial.Snw' failed with diagnostics:
 chunk 18 (label = geoInterpol) 
Error in tapply(intpl, list(grid[, 1], grid[, 2]), mean) : 
  arguments must have same length

--- failed re-building ‘resistance_tutorial.Snw’

SUMMARY: processing the following files failed:
  ‘phylin_tutorial.Snw’ ‘resistance_tutorial.Snw’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
Undeclared packages ‘future’, ‘geiger’, ‘caper’ in Rd xrefs
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
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: ‘rgdal’
  All declared Imports should be used.
Undeclared package ‘picante’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘cowplot’ ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘intergraph’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  11.0Mb
'LazyData' is specified without a 'data' directory
incident: no visible global function definition for ‘splinefun’
incident: no visible global function definition for ‘integrate’
phytoprod: no visible global function definition for ‘approx’
phytoprod: no visible global function definition for ‘splinefun’
phytoprod: no visible global function definition for ‘integrate’
reflectance: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx integrate splinefun
Consider adding
  importFrom("stats", "approx", "integrate", "splinefun")
to your NAMESPACE file.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Namespace in Imports field not imported from: ‘FrF2.catlg128’
  All declared Imports should be used.
Undeclared package ‘BsMD’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2048 marked UTF-8 strings
Running examples in ‘pins-Ex.R’ failed
The error most likely occurred in:

> ### Name: board_azure
> ### Title: Use an Azure Blob Storage Container as a board
> ### Aliases: board_azure
> 
> ### ** Examples
> 
> if (requireNamespace("AzureStor")) {
+   # Public access board
+   url <- "https://pins.blob.core.windows.net/public-data"
+   container <- AzureStor::blob_container(url)
+   board <- board_azure(container)
+   board %>% pin_read("mtcars")
+ }
Loading required namespace: AzureStor
Error: Destination file exists and overwrite is FALSE
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘pins-update.Rmd’ using rmarkdown
Quitting from lines 43-48 (pins-update.Rmd) 
Error: processing vignette 'pins-update.Rmd' failed with diagnostics:
`meta$type` must be a character vector.
--- failed re-building ‘pins-update.Rmd’

--- re-building ‘pins.Rmd’ using rmarkdown
Quitting from lines 233-237 (pins.Rmd) 
Error: processing vignette 'pins.Rmd' failed with diagnostics:
[EACCES] Failed to open '/data/gannet/ripley/.cache/pins/url/62ed70d133bdeb85a5123407645d5570/data.txt': permission denied
--- failed re-building ‘pins.Rmd’

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

SUMMARY: processing the following files failed:
  ‘pins-update.Rmd’ ‘pins.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
plot.pred.int: no visible global function definition for ‘plot.default’
plot.pred.int: no visible global function definition for ‘axis’
plot.pred.int: no visible global function definition for ‘box’
plot.pred.int : cidist: no visible global function definition for
  ‘ecdf’
plot.pred.int : negcidist: no visible global function definition for
  ‘ecdf’
plot.pred.int : pi.col.fun: no visible global function definition for
  ‘gray’
plot.pred.int: no visible global function definition for ‘segments’
plot.pred.int: no visible global function definition for ‘points’
plot.pred.int: no visible global function definition for ‘abline’
pred.int: no visible binding for global variable ‘sd’
prop.test.mult: no visible global function definition for ‘qnorm’
sim.basic: no visible global function definition for ‘rbinom’
sim.basic: no visible global function definition for ‘rnorm’
t.test.mult: no visible global function definition for ‘qt’
Undefined global functions or variables:
  abline axis box ecdf gray plot.default points qnorm qt rbinom rnorm
  sd segments
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "box", "plot.default",
             "points", "segments")
  importFrom("stats", "ecdf", "qnorm", "qt", "rbinom", "rnorm", "sd")
to your NAMESPACE file.
File ‘pirate/libs/pirate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘ggsubplot’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘Hmisc’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘usethis’ in Rd xrefs
Undeclared packages ‘pkgdown’, ‘htmlwidgets’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
PKmod: no visible global function definition for ‘deriv’
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
PKadjust: no visible binding for global variable ‘jpeg’
PKadjust: no visible binding for global variable ‘bmp’
PKadjust: no visible binding for global variable ‘png’
PKadjust: no visible binding for global variable ‘tiff’
PKadjust: no visible binding for global variable ‘dev.new’
PKadjust: no visible global function definition for ‘dev.off’
PKfigure: no visible global function definition for ‘dev.cur’
PKfigure: no visible global function definition for ‘dev.off’
PKoutput: no visible global function definition for ‘heatmap’
PKoutput: no visible global function definition for
  ‘packageDescription’
PKshow: no visible global function definition for ‘browseURL’
addList1: no visible global function definition for ‘formula’
addList1.old: no visible global function definition for ‘formula’
addList2: no visible global function definition for ‘formula’
generate.plot: no visible global function definition for ‘dev.off’
writeHTML: no visible global function definition for
  ‘packageDescription’
writeLst: no visible global function definition for
  ‘packageDescription’
writeLst.tab: no visible global function definition for
  ‘packageDescription’
writeTable: no visible global function definition for
  ‘packageDescription’
writeTable: no visible global function definition for ‘quantile’
initialize,nonmem: no visible global function definition for
  ‘read.table’
Undefined global functions or variables:
  bmp browseURL dev.cur dev.new dev.off formula heatmap jpeg
  packageDescription png quantile read.table tiff
Consider adding
  importFrom("grDevices", "bmp", "dev.cur", "dev.new", "dev.off", "jpeg",
             "png", "tiff")
  importFrom("stats", "formula", "heatmap", "quantile")
  importFrom("utils", "browseURL", "packageDescription", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘Indometh_Bolus_Linear_CoreOutput.txt’
  ‘Indometh_Bolus_Log_CoreOutput.txt’
  ‘Indometh_Infusion_Linear_CoreOutput.txt’
  ‘Indometh_Infusion_Log_CoreOutput.txt’ ‘Output’
  ‘Theoph_Linear_CoreOutput.txt’ ‘Theoph_Log_CoreOutput.txt’
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.7Mb
'LazyData' is specified without a 'data' directory
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.
Error(s) in re-building vignettes:
--- re-building ‘decay_rates.Rmd’ using knitr
--- finished re-building ‘decay_rates.Rmd’

--- re-building ‘fresnel.Rmd’ using knitr
--- finished re-building ‘fresnel.Rmd’

--- re-building ‘gaussian.rmd’ using knitr
Loading required package: dielectric
Warning in `[.data.frame`(x$env$data, 1L, drop = FALSE) :
  'drop' argument will be ignored
Quitting from lines 137-177 (gaussian.rmd) 
Error: processing vignette 'gaussian.rmd' failed with diagnostics:
'from' must be of length 1
--- failed re-building ‘gaussian.rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Note: found 150 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.html’ ‘P2Run.png’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
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.
'LazyData' is specified without a 'data' directory
bwfw.hmm: no visible global function definition for ‘dnorm’
bwfw1.hmm: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Rd file 'em.hmm.Rd':
  \examples lines wider than 100 characters:
     #all.Rlts=cbind(rbind(chr1.data,chr6.data), LIS=c(chr1.L2rlts$LIS,chr6.L2rlts$LIS), gFDR=plis.rlts$aLIS, fdr001state=plis.rlts$States)

These lines will be truncated in the PDF manual.
Namespaces in Imports field not imported from:
  ‘PlackettLuce’ ‘StatRank’ ‘pmr’ ‘prefmod’ ‘rankdist’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘Formula’ ‘sm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘plm-Ex.R’ failed
The error most likely occurred in:

> ### Name: is.pconsecutive
> ### Title: Check if time periods are consecutive
> ### Aliases: is.pconsecutive is.pconsecutive.default
> ###   is.pconsecutive.data.frame is.pconsecutive.pseries
> ###   is.pconsecutive.pdata.frame is.pconsecutive.panelmodel
> ### Keywords: attribute
> 
> ### ** Examples
> 
> 
> data("Grunfeld", package = "plm")
> is.pconsecutive(Grunfeld)
Error in is.pconsecutive.default(x_ordered, id_ordered, time_ordered,  : 
  arguments 'x', 'id', 'time' must have same length: length(x): 5, length(id): 200, length(time): 200
Calls: is.pconsecutive ... is.pconsecutive.data.frame -> is.pconsecutive.default
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   7.3Mb
Undeclared package ‘DESeq2’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
Note: found 12992 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘plothelper-Ex.R’ failed
The error most likely occurred in:

> ### Name: count_each_column
> ### Title: Counting Each Column and Summarizing in a Matrix
> ### Aliases: count_each_column
> 
> ### ** Examples
> 
> # values that do not appear in 
> # the data can also be counted.
> # a factor will be transformed into
> # a character variable automatically.
> x1=c("a", "b", "a", "b", NA)
> x2=factor(x1)
> x3=c("1", "3", "2", "1", "a")
> dat=data.frame(x1, x2, x3, stringsAsFactors=FALSE)
> res=count_each_column(dat, answer=c("c", "d", NA, "a"))
Error in splitter_a(.data, .margins, .expand) : Invalid margin
Calls: count_each_column -> unique -> unlist -> <Anonymous> -> splitter_a
Execution halted
Namespaces in Imports field not imported from:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.0Mb
Undeclared package ‘exams’ in Rd xrefs
Undeclared package ‘scape’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘patchwork’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running examples in ‘plotmo-Ex.R’ failed
The error most likely occurred in:

> ### Name: plotmo
> ### Title: Plot a model's response over a range of predictor values (the
> ###   model surface)
> ### Aliases: plotmo
> ### Keywords: partial dependence regression
> 
> ### ** Examples
> 
> if (require(rpart)) {
+     data(kyphosis)
+     rpart.model <- rpart(Kyphosis~., data=kyphosis)
+     # pass type="prob" to plotmo's internal calls to predict.rpart, and
+     # select the column named "present" from the matrix returned by predict.rpart
+     plotmo(rpart.model, type="prob", nresponse="present")
+ }
Loading required package: rpart
Error: nresponse="present" cannot be used because the predicted response is a vector (it has no columns)
Execution halted
Malformed Title field: should not end in a period.
generateEnvelope: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Rd file 'envelopeArea_and_Perimeter.Rd':
  \examples lines wider than 100 characters:
     cat("circle area = ", pi * r^2, " = ", sum(pi * r^2), "\ncircle perimenter = ",  2 * pi * r, " = ",  2 * pi * sum(r), "\n")

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

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

These lines will be truncated in the PDF manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
llla.bi: no visible global function definition for ‘as.formula’
llla.bi: no visible global function definition for ‘glm’
llla.bi: no visible global function definition for ‘binomial’
llla.bi: no visible binding for global variable ‘logit’
llla.bi: no visible global function definition for ‘vcov’
llla.bi: no visible global function definition for ‘coef’
llla.mc: no visible global function definition for ‘model.matrix’
llla.mc: no visible global function definition for ‘as.formula’
llla.mc: no visible global function definition for ‘coxph’
llla.mc: no visible global function definition for ‘vcov’
llla.mc: no visible global function definition for ‘coef’
llla.mle: no visible global function definition for ‘as.formula’
llla.mle: no visible global function definition for ‘glm’
llla.mle: no visible global function definition for ‘poisson’
llla.mle: no visible global function definition for ‘coef’
llla.mle: no visible global function definition for ‘vcov’
mclgen: no visible global function definition for ‘reshape’
simRasch.1D: no visible global function definition for ‘rnorm’
simRasch.1D: no visible global function definition for ‘runif’
vcov.sandwich.glm: no visible global function definition for
  ‘model.matrix’
vcov.sandwich.glm: no visible global function definition for ‘weights’
vcov.sandwich.glm: no visible global function definition for
  ‘residuals’
vcov.sandwich.glm: no visible global function definition for ‘vcov’
Undefined global functions or variables:
  as.formula binomial coef coxph glm logit model.matrix poisson reshape
  residuals rnorm runif vcov weights
Consider adding
  importFrom("stats", "as.formula", "binomial", "coef", "glm",
             "model.matrix", "poisson", "reshape", "residuals", "rnorm",
             "runif", "vcov", "weights")
to your NAMESPACE file.
Package suggested but not available for checking: ‘plspm’
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’
  Running ‘testthat.R’ [10s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(plsmod)
  Loading required package: parsnip
  > 
  > test_check("plsmod")
  keepX is of length 4 while ncomp is 3 
  trimming keepX to [33mc(4,4,4)[39mkeepX is of length 4 while ncomp is 3 
  trimming keepX to [33mc(2,2,2)[39mkeepX is of length 4 while ncomp is 3 
  trimming keepX to [33mc(2,2,2)[39mkeepX is of length 100 while ncomp is 3 
  trimming keepX to [33mc(100,100,100)[39mkeepX is of length 100 while ncomp is 3 
  trimming keepX to [33mc(100,100,100)[39mkeepX is of length 8 while ncomp is 3 
  trimming keepX to [33mc(8,8,8)[39mkeepX is of length 100 while ncomp is 3 
  trimming keepX to [33mc(100,100,100)[39mkeepX is of length 100 while ncomp is 3 
  trimming keepX to [33mc(100,100,100)[39mkeepX is of length 100 while ncomp is 3 
  trimming keepX to [33mc(100,100,100)[39mkeepX is of length 100 while ncomp is 3 
  trimming keepX to [33mc(100,100,100)[39m══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-class-pls.R:51:3): classification model fitting ───────────────
  parsnip_pls_da_class[[1]] not equal to `uni_model_pred`.
  Lengths: 1, 10
  10 NA mismatches
  ── Failure (test-class-spls.R:52:3): classification model fitting ──────────────
  parsnip_spls_da_class[[1]] not equal to `uni_model_pred`.
  Lengths: 1, 10
  10 NA mismatches
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 72 ]
  Error: Test failures
  Execution halted
Undeclared package ‘sm’ in Rd xrefs
print.densityEHpi: no visible global function definition for ‘str’
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
File ‘plugdensity/libs/plugdensity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ssh’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘glue’
  All declared Imports should be used.
Rd file 'predict.plus.Rd':
  \examples lines wider than 100 characters:
     extracted.values <- predict(object, lam = sort(object$lam.path[1:10],decreasing=TRUE), newx=object$x)

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
Running examples in ‘plyr-Ex.R’ failed
The error most likely occurred in:

> ### Name: mdply
> ### Title: Call function with arguments in array or data frame, returning a
> ###   data frame.
> ### Aliases: mdply
> ### Keywords: manip
> 
> ### ** Examples
> 
> mdply(data.frame(mean = 1:5, sd = 1:5), rnorm, n = 2)
Warning in `[.data.frame`(x$env$data, 1L, drop = FALSE) :
  'drop' argument will be ignored
Warning in `[.data.frame`(x$env$data, 2L, drop = FALSE) :
  'drop' argument will be ignored
Error in list_to_dataframe(res, attr(.data, "split_labels"), .id, id_as_factor) : 
  nrow(labels) == length(null) is not TRUE
Calls: mdply -> adply -> ldply -> list_to_dataframe -> stopifnot
Execution halted
Malformed Description field: should contain one or more complete sentences.
.MCM: no visible global function definition for ‘runif’
.MCM: no visible global function definition for ‘rmultinom’
.MCM: no visible global function definition for ‘mahalanobis’
.MCM: no visible global function definition for ‘optimize’
.MCM : f: no visible global function definition for ‘mahalanobis’
.MCM: no visible global function definition for ‘alarm’
.igpark: no visible global function definition for ‘kmeans’
.loglik: no visible global function definition for ‘mahalanobis’
.plot.gpcm: no visible global function definition for ‘lines’
.plot.gpcm: no visible global function definition for ‘legend’
.rwgpar: no visible global function definition for ‘rexp’
.weights: no visible global function definition for ‘mahalanobis’
Undefined global functions or variables:
  alarm kmeans legend lines mahalanobis optimize rexp rmultinom runif
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "kmeans", "mahalanobis", "optimize", "rexp",
             "rmultinom", "runif")
  importFrom("utils", "alarm")
to your NAMESPACE file.
Note: found 62 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Running examples in ‘pmml-Ex.R’ failed
The error most likely occurred in:

> ### Name: add_data_field_attributes
> ### Title: Add attribute values to an existing DataField element in a given
> ###   PMML file
> ### Aliases: add_data_field_attributes
> ### Keywords: interface
> 
> ### ** Examples
> 
> # Make a sample model:
> fit <- lm(Sepal.Length ~ ., data = iris[, -5])
> fit_pmml <- pmml(fit)
> 
> # The resulting model has mining fields with no information besides
> # fieldName, dataType and optype. This object is already an xml
> # node (not an external text file), so there is no need to convert
> # it to an xml node object.
> 
> # Create data frame with attribute information:
> 
> attributes <- data.frame(c("FlowerWidth", 1), c("FlowerLength", 0),
+   stringsAsFactors = FALSE
+ )
> rownames(attributes) <- c("displayName", "isCyclic")
> colnames(attributes) <- c("Sepal.Width", "Petal.Length")
> 
> # Although not needed in this first try, necessary to easily add
> # new values later. Removes values as factors so that new values
> # added later are not evaluated as factor values and thus rejected
> # as invalid.
> attributes[] <- lapply(attributes, as.character)
> 
> fit_pmml_2 <- add_data_field_attributes(fit_pmml,
+   attributes,
+   namespace = "4_4"
+ )
Error in getNodeSet(dd, paste0("p:DataField[@name='", colnames(attributes)[i],  : 
  subscript out of bounds
Calls: add_data_field_attributes
Execution halted
Running ‘testthat.R’ [81s/101s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pmml, quietly = T)
  > 
  > test_check("pmml")
  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).
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (49)
  • skip (2)
  • skip until export issue is resolved (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_add_data_field_attributes.R:37:3): Error when field additions are not in model ──
  `add_data_field_attributes(fit_pmml, attributes_2, namespace = "4_4")` threw an error with unexpected message.
  Expected match: "The following field additions are not in the model: FooBar, raBooF"
  Actual message: "subscript out of bounds"
  Backtrace:
      █
   1. ├─testthat::expect_error(...) test_add_data_field_attributes.R:37:2
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat:::.capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─pmml::add_data_field_attributes(fit_pmml, attributes_2, namespace = "4_4")
  
  [ FAIL 1 | WARN 1 | SKIP 52 | PASS 376 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
dbm: no visible global function definition for ‘optim’
dbm: no visible global function definition for ‘new’
destat: no visible global function definition for ‘weighted.mean’
local.knn: no visible global function definition for ‘sd’
local.knn: no visible global function definition for ‘optim’
mdpref: no visible global function definition for ‘sd’
mdpref: no visible global function definition for ‘text’
mdpref: no visible global function definition for ‘lines’
phicom: no visible global function definition for ‘optim’
phicom: no visible global function definition for ‘new’
pl: no visible global function definition for ‘optim’
pl: no visible global function definition for ‘new’
rol: no visible global function definition for ‘nlm’
rol: no visible global function definition for ‘new’
wdbm: no visible global function definition for ‘optim’
wdbm: no visible global function definition for ‘new’
Undefined global functions or variables:
  lines new nlm optim sd text weighted.mean
Consider adding
  importFrom("graphics", "lines", "text")
  importFrom("methods", "new")
  importFrom("stats", "nlm", "optim", "sd", "weighted.mean")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ggrepel’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pnmtrem1: no visible global function definition for ‘pnorm’
pnmtrem1: no visible global function definition for ‘dnorm’
pnmtrem1: no visible global function definition for ‘ginv’
pnmtrem1 : fun: no visible global function definition for ‘pnorm’
pnmtrem1 : derf: no visible global function definition for ‘dnorm’
pnmtrem1 : derf: no visible global function definition for ‘pnorm’
pnmtrem1 : fun: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm ginv pnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘TODO.md’
'library' or 'require' call to ‘rgenoud’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
smooth: no visible global function definition for ‘genoud’
Undefined global functions or variables:
  genoud
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘abc’ ‘doParallel’ ‘gdistance’ ‘geosphere’ ‘lhs’ ‘metRology’ ‘raster’
  ‘trend’
  All declared Imports should be used.
Note: found 7256 marked UTF-8 strings
bipoilogMLE: no visible global function definition for ‘optim’
bipoilogMLE: no visible global function definition for ‘write.table’
poilogMLE: no visible global function definition for ‘optim’
rbipoilog : sim: no visible global function definition for ‘rnorm’
rbipoilog : sim: no visible global function definition for ‘rpois’
rpoilog : sim: no visible global function definition for ‘rnorm’
rpoilog : sim: no visible global function definition for ‘rpois’
Undefined global functions or variables:
  optim rnorm rpois write.table
Consider adding
  importFrom("stats", "optim", "rnorm", "rpois")
  importFrom("utils", "write.table")
to your NAMESPACE file.
File ‘poilog/libs/poilog.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘car’ ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘ISOcodes’ in Rd xrefs
Note: found 8 marked UTF-8 strings
approxMargMLE: no visible global function definition for ‘optim’
approxMargMLECI : ciFunction: no visible global function definition for
  ‘qchisq’
approxMargMLECI: no visible global function definition for ‘uniroot’
margMLE: no visible global function definition for ‘optim’
margMLECI: no visible global function definition for ‘optim’
margMLECI : unNormLikeMinusVal: no visible global function definition
  for ‘qchisq’
margMLECI: no visible global function definition for ‘uniroot’
profMLECI : ciFunction: no visible global function definition for
  ‘qchisq’
profMLECI: no visible global function definition for ‘uniroot’
rtbinom: no visible global function definition for ‘rbinom’
rtpois: no visible global function definition for ‘rpois’
waldCI: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  optim qchisq qnorm rbinom rpois uniroot
Consider adding
  importFrom("stats", "optim", "qchisq", "qnorm", "rbinom", "rpois",
             "uniroot")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
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.
Undeclared packages ‘workflows’, ‘rstanarm’, ‘rstan’ in Rd xrefs
Running ‘spelling.R’
  Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(poissonreg)
  Loading required package: parsnip
  > 
  > test_check("poissonreg")
  
  Attaching package: 'rlang'
  
  The following objects are masked from 'package:testthat':
  
      is_false, is_null, is_true
  
  
  Attaching package: 'tidyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (4)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-poisson-reg.R:174:3): glm execution ───────────────────────────
  `... <- NULL` threw an error.
  Message: `x` cannot be a vector.
  Class:   rlang_error/error/condition
  Backtrace:
      █
   1. ├─testthat::expect_error(...) test-poisson-reg.R:174:2
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat:::.capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. ├─generics::fit_xy(...)
   7. └─parsnip::fit_xy.model_spec(...)
   8.   └─parsnip:::xy_form(...)
   9.     └─parsnip::.convert_xy_to_form_fit(...)
  ── Error (test-poisson-reg.R:199:3): glm prediction ────────────────────────────
  Error: `x` cannot be a vector.
  Backtrace:
      █
   1. ├─generics::fit_xy(...) test-poisson-reg.R:199:2
   2. └─parsnip::fit_xy.model_spec(...)
   3.   └─parsnip:::xy_form(...)
   4.     └─parsnip::.convert_xy_to_form_fit(...)
  ── Error (test-poisson-reg.R:219:3): newdata error trapping ────────────────────
  Error: `x` cannot be a vector.
  Backtrace:
      █
   1. ├─generics::fit_xy(...) test-poisson-reg.R:219:2
   2. └─parsnip::fit_xy.model_spec(...)
   3.   └─parsnip:::xy_form(...)
   4.     └─parsnip::.convert_xy_to_form_fit(...)
  
  [ FAIL 3 | WARN 0 | SKIP 4 | PASS 32 ]
  Error: Test failures
  Execution halted
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Packages in Depends field not imported from:
  ‘combinat’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Est.Depth: no visible global function definition for ‘quantile’
PS.FDR: no visible global function definition for ‘quantile’
Permu.Ind: no visible global function definition for ‘permn’
Permu.Ind: no visible global function definition for ‘hcube’
Trans.Data: no visible global function definition for ‘write.table’
Trans.Data: no visible global function definition for ‘predict’
Trans.Data: no visible global function definition for ‘lm’
Undefined global functions or variables:
  hcube lm permn predict quantile write.table
Consider adding
  importFrom("stats", "lm", "predict", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘pow.txt’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘argonDash’ ‘argonR’ ‘colourpicker’ ‘ggplot2’ ‘grid’ ‘hexSticker’
  ‘png’ ‘shinyWidgets’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages in Depends field not imported from:
  ‘MASS’ ‘scatterplot3d’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.poLCA: no visible global function definition for ‘layout’
plot.poLCA: no visible global function definition for ‘par’
poLCA: no visible global function definition for ‘model.frame’
poLCA: no visible global function definition for ‘model.response’
poLCA: no visible global function definition for ‘model.matrix’
poLCA: no visible global function definition for ‘runif’
poLCA: no visible global function definition for ‘ginv’
poLCA: no visible global function definition for ‘flush.console’
poLCA.makeplot.dich: no visible global function definition for
  ‘scatterplot3d’
poLCA.makeplot.poly: no visible global function definition for
  ‘scatterplot3d’
poLCA.se: no visible global function definition for ‘ginv’
poLCA.simdata: no visible global function definition for ‘runif’
poLCA.simdata: no visible global function definition for ‘rnorm’
poLCA.table: no visible global function definition for ‘model.frame’
print.poLCA: no visible global function definition for ‘pt’
print.poLCA: no visible global function definition for ‘flush.console’
rmulti: no visible global function definition for ‘runif’
Undefined global functions or variables:
  flush.console ginv layout model.frame model.matrix model.response par
  pt rnorm runif scatterplot3d
Consider adding
  importFrom("graphics", "layout", "par")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "pt", "rnorm", "runif")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Undeclared package ‘flexmix’ in Rd xrefs
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.
Note: found 21 marked UTF-8 strings
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Note: found 52 marked UTF-8 strings
Undeclared package ‘purrr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pollimetrydata’
'LazyData' is specified without a 'data' directory
qPolyaAeppliSingle: no visible global function definition for ‘qgamma’
rPolyaAeppli: no visible global function definition for ‘rpois’
rPolyaAeppli: no visible global function definition for ‘rgeom’
Undefined global functions or variables:
  qgamma rgeom rpois
Consider adding
  importFrom("stats", "qgamma", "rgeom", "rpois")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
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.
Found the following files/directories:
  ‘polyfreqs-mcmc.out’
Running examples in ‘PolyHaplotyper-Ex.R’ failed
The error most likely occurred in:

> ### Name: checkmrkDosage
> ### Title: check a marker dosages matrix or data.frame
> ### Aliases: checkmrkDosage
> 
> ### ** Examples
> 
> mrkdos <- data.frame(
+  marker=paste0("mrk", 1:3),
+  indiv1=c(1, 2, 2),
+  indiv2=c(4, 0, 0),
+  indiv3=c(3, 0, 2))
> # use all rows and columns:
> checkmrkDosage(mrkDosage=mrkdos, ploidy=4)
Error in dimnames(x) <- dn : 
  length of 'dimnames' [2] not equal to array extent
Calls: checkmrkDosage -> colnames<-
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘PolyHaplotyper.Rmd’ using rmarkdown
Quitting from lines 142-147 (PolyHaplotyper.Rmd) 
Error: processing vignette 'PolyHaplotyper.Rmd' failed with diagnostics:
length of 'dimnames' [2] not equal to array extent
--- failed re-building ‘PolyHaplotyper.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    R      6.5Mb
    data   4.6Mb
Found the following files/directories:
  ‘AbsorbedDrugMetabolites’ ‘CorrelationResults’
  ‘EndogenousMetabolites’ ‘HeatMap’ ‘PKresults’
  ‘SecondAbsorbedMetabolites’ ‘preprocessed-data’
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    1.7Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
    libs      3.3Mb
Undeclared packages ‘polymapR’, ‘BSgenome’ in Rd xrefs
Running examples in ‘polyreg-Ex.R’ failed
The error most likely occurred in:

> ### Name: FSR
> ### Title: FSR
> ### Aliases: FSR print.FSR summary.FSR
> 
> ### ** Examples
> 
> out <- FSR(mtcars)
set seed to 66608964.

Error in which(x_factors) : argument to 'which' is not logical
Calls: FSR -> which
Execution halted
Undeclared package ‘Rcmdr’ in Rd xrefs
Found the following files/directories:
  ‘test-data.R’ ‘test-inits.R’ ‘test.bug’ ‘test.cmd’
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘matrixcalc’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘matrixcalc’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
print.mixed.pom: no visible global function definition for ‘pnorm’
print.pom: no visible global function definition for ‘pnorm’
siteocc : get.mod.matrix: no visible binding for global variable
  ‘na.pass’
siteocc : get.mod.matrix: no visible global function definition for
  ‘formula’
siteocc : get.mod.matrix: no visible global function definition for
  ‘model.matrix’
siteocc: no visible global function definition for ‘nlminb’
siteocc: no visible global function definition for
  ‘is.positive.definite’
Undefined global functions or variables:
  formula is.positive.definite model.matrix na.pass nlminb pnorm
Consider adding
  importFrom("stats", "formula", "model.matrix", "na.pass", "nlminb",
             "pnorm")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 44.2Mb
  sub-directories of 1Mb or more:
    libs  43.8Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Non-standard file/directory found at top level:
  ‘extdata’
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Rd file 'popgen.Rd':
  \usage lines wider than 90 characters:
     popgen(datafile, ndigit = 3, freq.overall = T, freq.by.pop = T, genetic.stats = T, pairwise.fst = T)

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘WhopGenome’
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Undeclared package ‘ecodist’ in Rd xrefs
asymmetricIntervals: no visible global function definition for ‘stack’
bonferroniIntervals: no visible global function definition for ‘stack’
bonferroniIntervals: no visible global function definition for ‘lm’
bonferroniIntervals: no visible global function definition for
  ‘predict’
bootstrapIntervals: no visible global function definition for ‘stack’
component1a: no visible global function definition for ‘pnorm’
component1b: no visible global function definition for ‘pnorm’
component2: no visible global function definition for ‘dgamma’
eqnForMin: no visible global function definition for ‘pnorm’
eqnForMin: no visible global function definition for ‘integrate’
integrand : <anonymous>: no visible global function definition for
  ‘pnorm’
integrand: no visible global function definition for ‘dnorm’
integrate2: no visible global function definition for ‘integrate’
integrate2a: no visible global function definition for ‘integrate’
integrate2b: no visible global function definition for ‘integrate’
integrate4a: no visible global function definition for ‘integrate’
integrate4b: no visible global function definition for ‘integrate’
optimalCScalar2: no visible global function definition for ‘uniroot’
optimalLambda: no visible global function definition for ‘optimise’
optimalLambdaC: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dgamma dnorm integrate lm optimise pnorm predict stack uniroot
Consider adding
  importFrom("stats", "dgamma", "dnorm", "integrate", "lm", "optimise",
             "pnorm", "predict", "uniroot")
  importFrom("utils", "stack")
to your NAMESPACE file.
Error(s) in re-building vignettes:
--- re-building ‘algo.Rnw’ using knitr
Loading required package: adegenet
Loading required package: ade4

   /// adegenet 2.1.5 is loaded ////////////

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


This is poppr version 2.9.3. To get started, type package?poppr
OMP parallel support: available
Warning in infinite_vals_replacement(D, warning) :
  Infinite values detected.
Error: processing vignette 'algo.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'algo.tex' failed.
LaTeX errors:
! Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
--- failed re-building ‘algo.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Running examples in ‘popsom-Ex.R’ failed
The error most likely occurred in:

> ### Name: fitted
> ### Title: Fit Observations
> ### Aliases: fitted
> 
> ### ** Examples
> 
> data(iris)
> 
> df <- subset(iris,select=-Species)
> labels <- subset(iris,select=Species)
> 
> m <- map(df,labels,xdim=15,ydim=10,train=10000)
Error in centroids[[ix, iy]] : subscript out of bounds
Calls: map -> majority.labels
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Undeclared packages ‘rags2ridges’, ‘ragt2ridges’ in Rd xrefs
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘TSA’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘bslib’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘StanHeaders’ ‘dplyr’ ‘ggplot2’ ‘gridExtra’ ‘rstan’ ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ActCR’ ‘ActFrag’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘rstan’, ‘R2WinBUGS’, ‘R2jags’, ‘R2OpenBUGS’, ‘nimble’, ‘rjags’, ‘jagsUI’ in Rd xrefs
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘tcltk’ which was already attached by Depends.
  Please remove these calls from your code.
fnfam: no visible global function definition for ‘qnorm’
fx: no visible global function definition for ‘qnorm’
normplot : <local> : replot: no visible global function definition for
  ‘qnorm’
normplot : <local> : replot: no visible global function definition for
  ‘pnorm’
normplot : <local> : replot: no visible global function definition for
  ‘dnorm’
normplot : <local> : replot: no visible global function definition for
  ‘points’
normplot : <local> : replot: no visible global function definition for
  ‘lines’
normplot : <local> : regen: no visible global function definition for
  ‘rnorm’
normplot : <local> : regen: no visible global function definition for
  ‘rexp’
nsibs: no visible global function definition for ‘qnorm’
ntdt: no visible global function definition for ‘uniroot’
plotNtdt: no visible global function definition for ‘lines’
plotNtdt: no visible global function definition for ‘legend’
ptdt: no visible global function definition for ‘optimize’
ptdt: no visible global function definition for ‘uniroot’
ptdt: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm legend lines optimize pnorm points qnorm rexp rnorm uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "points")
  importFrom("stats", "dnorm", "optimize", "pnorm", "qnorm", "rexp",
             "rnorm", "uniroot")
to your NAMESPACE file.
Running examples in ‘PoweR-Ex.R’ failed
The error most likely occurred in:

> ### Name: powcomp.fast
> ### Title: Computation of power and level tables for hypothesis tests.
> ### Aliases: powcomp.fast
> ### Keywords: datagen htest
> 
> ### ** Examples
> 
> ## Regenerate Table 6 from Puig (2000) (page 424)
> 
> law.index <- 1
> # Take M = 50000 for accurate results 
> M <- 10
> vectn <- c(10,15,20,35,50,75,100)
> level <- c(0.05)
> stat.indices <- c(43,44,42,45,46)
> law.indices <- c(2,3,4)
> alter <- list(stat43 = 3,stat44 = 3,stat42 = 3,stat45 = 3,stat46 = 3)
> critval <- many.crit(law.index,stat.indices,M,vectn,level,alter,
+                      law.pars = NULL,parstats = NULL)
> table6 <- powcomp.fast(law.indices,stat.indices,vectn,M,level,critval = critval,alter,
+                        parlaws = NULL,parstats = NULL,nbclus = 1)
> table6
Error in t2[j + nbvectn * (i - 1), ] <- average_power(mytable, levels[i],  : 
  number of items to replace is not a multiple of replacement length
Calls: <Anonymous> -> print.power -> print -> print.power1
Execution halted
Undeclared package ‘advclust’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc  12.0Mb
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Namespaces in Imports field not imported from:
  ‘rpart’ ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘dev’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lmtest’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
TT.test : <anonymous>: no visible global function definition for
  ‘t.test’
TT.test: no visible binding for global variable ‘sd’
TT.test: no visible global function definition for ‘setNames’
kirjelda : combo: no visible binding for global variable ‘sd’
kor.tabel: no visible binding for global variable ‘cor.test’
Undefined global functions or variables:
  cor.test sd setNames t.test
Consider adding
  importFrom("stats", "cor.test", "sd", "setNames", "t.test")
to your NAMESPACE file.
File ‘prclust/libs/prclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘class’ ‘forcats’ ‘irr’ ‘lpSolve’ ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘docopt’ ‘here’ ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘TH.data’ ‘moonBook’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
gausspred: no visible global function definition for ‘qt’
mvapred: no visible global function definition for ‘qt’
Undefined global functions or variables:
  qt
Consider adding
  importFrom("stats", "qt")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Non-standard file/directory found at top level:
  ‘DESCRIPTION.bck’
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘predmixcor/R/firstlib.r’:
  .First.lib calls:
    cat("predmixcor loaded\n", "COPY RIGHT: Longhai Li\n", "http://math.usask.ca/~longhai\n",     "Type ?begin.predmixcor for help\n", sep = "")

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

Predict.mix: no visible global function definition for ‘dbinom’
abs_cor: no visible global function definition for ‘cor’
gen.alpha.IGamma: no visible global function definition for ‘qgamma’
gendata.mix: no visible global function definition for ‘runif’
gendata.mix: no visible global function definition for ‘rbeta’
mh1.unif: no visible global function definition for ‘runif’
train_predict_mix: no visible global function definition for ‘dbinom’
training: no visible global function definition for ‘runif’
training: no visible global function definition for ‘dbinom’
Undefined global functions or variables:
  cor dbinom qgamma rbeta runif
Consider adding
  importFrom("stats", "cor", "dbinom", "qgamma", "rbeta", "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘pkgdown’ ‘rmarkdown’
  All declared Imports should be used.
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘dplyr’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘colorspace’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Note: found 36 marked UTF-8 strings
Malformed Title field: should not end in a period.
Non-standard file/directory found at top level:
  ‘COPYRIGHTS’
Copyright information should be in file inst/COPYRIGHTS
Namespace in Imports field not imported from: ‘badger’
  All declared Imports should be used.
Note: found 42966 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    shinyApp   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘parsnip’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Running examples in ‘prettymapr-Ex.R’ failed
The error most likely occurred in:

> ### Name: mergebbox
> ### Title: Combine bounding boxes
> ### Aliases: mergebbox
> 
> ### ** Examples
> 
> box1 <- searchbbox("wolfville, ns")
Using default API key for pickpoint.io. If batch geocoding, please get your own (free) API key at https://app.pickpoint.io/sign-up
Warning in `[.data.frame`(x$env$data, 1L, drop = FALSE) :
  'drop' argument will be ignored
Warning in `[.data.frame`(x$env$data, 1L, drop = FALSE) :
  'drop' argument will be ignored
Error in data[[row$rank]] : 
  attempt to select less than one element in get1index
Calls: searchbbox ... ldply -> llply -> loop_apply -> <Anonymous> -> .fun
Execution halted
Found the following files/directories:
  ‘hista.png’ ‘plotcd.png’ ‘test.R’ ‘test.html’ ‘testR2html.R’
  ‘testglm.csv’ ‘testglm.html’ ‘testglm.tab’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘lubridate’
  All declared Imports should be used.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
File ‘PRIMAL/libs/PRIMAL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Running examples in ‘prim-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot.prim
> ### Title: PRIM plot for multivariate data
> ### Aliases: plot.prim
> ### Keywords: hplot
> 
> ### ** Examples
> 
> ## see ?predict.prim for bivariate example
> ## trivariate example
> data(quasiflow)
> qf <- quasiflow[1:1000,1:3]
> qf.label <- quasiflow[1:1000,4]
> thr <- c(0.25, -0.3)
> qf.prim <- prim.box(x=qf, y=qf.label, threshold=thr, threshold.type=0)
Warning in prim.combine(prim.pos, prim.neg, y.fun = y.fun) :
  Class boundaries overlap - will return NULL
Error in 1:m : argument of length 0
Calls: prim.box -> prim.which.box
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘prim-2d.Rmd’ using rmarkdown
Quitting from lines 27-33 (prim-2d.Rmd) 
Error: processing vignette 'prim-2d.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘prim-2d.Rmd’

--- re-building ‘prim-3d.Rmd’ using rmarkdown
Quitting from lines 60-62 (prim-3d.Rmd) 
Error: processing vignette 'prim-3d.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘prim-3d.Rmd’

SUMMARY: processing the following files failed:
  ‘prim-2d.Rmd’ ‘prim-3d.Rmd’

Error: Vignette re-building failed.
Execution halted
basisplot: no visible global function definition for ‘abline’
basisplot: no visible global function definition for ‘text’
basisplot: no visible global function definition for ‘par’
plot.prinsimp: no visible global function definition for ‘screeplot’
plot.simpart: no visible global function definition for ‘par’
position_text: no visible global function definition for ‘par’
position_text: no visible global function definition for ‘strwidth’
simpart.formula: no visible global function definition for ‘terms’
simpart.formula: no visible global function definition for
  ‘model.matrix’
varperc: no visible global function definition for ‘lines’
varperc: no visible global function definition for ‘text’
varsimp: no visible global function definition for ‘points’
varsimp: no visible global function definition for ‘text’
varsimp: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline lines model.matrix par points screeplot strwidth terms text
Consider adding
  importFrom("graphics", "abline", "lines", "par", "points", "strwidth",
             "text")
  importFrom("stats", "model.matrix", "screeplot", "terms")
to your NAMESPACE file.
Found the following files/directories:
  ‘network.html’ ‘network_files’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    3.4Mb
    libs  13.3Mb
Namespace in Imports field not imported from: ‘exactextractr’
  All declared Imports should be used.
Undeclared packages ‘ipflasso’, ‘mvtnorm’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘DT’ ‘rio’ ‘shiny’ ‘shinyjs’ ‘utils’ ‘webp’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
pr.conditional: no visible global function definition for ‘qnorm’
pr.marginal: no visible global function definition for ‘qnorm’
prLogisticDelta: no visible global function definition for ‘glm’
prLogisticDelta: no visible binding for global variable ‘binomial’
Undefined global functions or variables:
  binomial glm qnorm
Consider adding
  importFrom("stats", "binomial", "glm", "qnorm")
to your NAMESPACE file.
Package suggested but not available for checking: ‘ggpattern’
.pfda.fstep: no visible global function definition for ‘dist’
.pfda.mstep: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov dist
Consider adding
  importFrom("stats", "cov", "dist")
to your NAMESPACE file.
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
Suggests orphaned package: ‘bibtex’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘LaplacesDemon’ ‘epitools’ ‘rpivotTable’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    doc          11.1Mb
    htmlwidgets   2.6Mb
'LazyData' is specified without a 'data' directory
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
GPois: no visible global function definition for ‘dnorm’
GPois: no visible binding for global variable ‘poisson’
GPois: no visible global function definition for ‘predict’
GPois: no visible global function definition for ‘fitted’
GPois: no visible global function definition for ‘residuals’
GPois: no visible global function definition for ‘smooth.spline’
ProDenICA: no visible global function definition for ‘rnorm’
d.gaussmix: no visible global function definition for ‘dnorm’
djordan: no visible global function definition for ‘dt’
djordan: no visible global function definition for ‘dunif’
mixmat: no visible global function definition for ‘rnorm’
mixmat: no visible global function definition for ‘runif’
r.gaussmix: no visible global function definition for ‘rmultinom’
r.gaussmix: no visible global function definition for ‘rnorm’
rjordan: no visible global function definition for ‘rt’
rjordan: no visible global function definition for ‘runif’
rmix.dexp: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dnorm dt dunif fitted poisson predict residuals rmultinom rnorm rt
  runif smooth.spline
Consider adding
  importFrom("stats", "dnorm", "dt", "dunif", "fitted", "poisson",
             "predict", "residuals", "rmultinom", "rnorm", "rt", "runif",
             "smooth.spline")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘MASS’ ‘nlme’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'LazyData' is specified without a 'data' directory
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    extdata   7.4Mb
    libs      4.5Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   1.2Mb
    libs      2.4Mb
Packages in Depends field not imported from:
  ‘splines’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
IndividualPROC: no visible global function definition for ‘survfit’
IndividualPROC: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile survfit
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
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.
Running ‘testthat.R’ [10s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(distcrete)
  > library(incidence)
  > library(projections)
  > library(outbreaks)
  > library(magrittr)
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  > 
  > test_check("projections")
  Saving 7 x 7 in image
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (19)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-project.R:321:3): Test instantaneous_R = TRUE ───────────────────
  Error in `data.frame(local = I_tmp, imported = rep(0, length(I_tmp)))`: arguments imply differing number of rows: 51, 2
  Backtrace:
      █
   1. └─EpiEstim::estimate_R(...) test-project.R:321:2
   2.   └─EpiEstim:::estimate_R_func(...)
   3.     └─EpiEstim:::posterior_from_si_distr(...)
   4.       └─EpiEstim::overall_infectivity(incid, si_distr)
   5.         └─EpiEstim:::process_I(incid)
   6.           └─base::data.frame(local = I_tmp, imported = rep(0, length(I_tmp)))
  
  [ FAIL 1 | WARN 0 | SKIP 19 | PASS 75 ]
  Deleting unused snapshots:
  * plots/basic-example-plot.svg
  * plots/evd-proj-box-no-outliers.svg
  * plots/evd-proj-box-only.svg
  * plots/evd-proj-full-red-ribbon-narrow-range.svg
  * plots/evd-proj-no-box-custom-lines.svg
  * plots/evd-proj-no-ribbon.svg
  * plots/evd-proj-red-box.svg
  * plots/evd-proj-red-ribbon.svg
  * plots/evd-proj-ribbon-only.svg
  * plots/evd-proj-with-incidence-incidence-and-custom.svg
  * plots/evd-proj-with-incidence-incidence-box-only.svg
  * plots/evd-proj-with-incidence-incidence-no-box.svg
  * plots/evd-proj-with-incidence-incidence.svg
  * plots/evd-proj.svg
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘optimx’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
Namespaces in Imports field not imported from:
  ‘StanHeaders’ ‘methods’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Undeclared packages ‘binom’, ‘PropCIs’, ‘BlakerCI’, ‘prevalence’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SDMTools’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   2.7Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
addpi: no visible global function definition for ‘lines’
genPerms: no visible global function definition for ‘combn’
getVar: no visible global function definition for ‘glm’
getVar: no visible global function definition for ‘binomial’
getVar: no visible global function definition for ‘var’
pba: no visible global function definition for ‘glm’
pba: no visible global function definition for ‘binomial’
pba: no visible global function definition for ‘predict’
pba: no visible global function definition for ‘rbinom’
pcr: no visible global function definition for ‘quantile’
plotpi: no visible global function definition for ‘axis’
plotpi: no visible global function definition for ‘abline’
plotpi: no visible global function definition for ‘lines’
Undefined global functions or variables:
  abline axis binomial combn glm lines predict quantile rbinom var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "binomial", "glm", "predict", "quantile", "rbinom",
             "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grDevices’
  All declared Imports should be used.
Package in Depends field not imported from: ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
addIonSatistics: no visible binding for global variable ‘median’
adjustOne: no visible binding for global variable ‘median’
attachModifications: no visible global function definition for
  ‘na.omit’
avrgLoadingCalculation: no visible binding for global variable ‘median’
channelResponses : estimate: no visible binding for global variable
  ‘var’
responseStatisics : func: no visible global function definition for
  ‘aggregate’
testing: no visible global function definition for ‘aov’
testingOneshot: no visible global function definition for ‘anova’
testingTukey: no visible global function definition for ‘TukeyHSD’
Undefined global functions or variables:
  TukeyHSD aggregate anova aov median na.omit var
Consider adding
  importFrom("stats", "TukeyHSD", "aggregate", "anova", "aov", "median",
             "na.omit", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘class’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘class’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
addcircle: no visible global function definition for ‘lines’
addclassifierboundary: no visible global function definition for ‘par’
addclassifierboundary: no visible global function definition for
  ‘contour’
plot.protoclass: no visible global function definition for ‘box’
plot.protoclass: no visible global function definition for ‘rgb2hsv’
plot.protoclass: no visible global function definition for ‘col2rgb’
plot.protoclass: no visible global function definition for ‘points’
plot.protoclass: no visible global function definition for ‘hsv’
predict.protoclass: no visible global function definition for ‘knn1’
Undefined global functions or variables:
  box col2rgb contour hsv knn1 lines par points rgb2hsv
Consider adding
  importFrom("grDevices", "col2rgb", "hsv", "rgb2hsv")
  importFrom("graphics", "box", "contour", "lines", "par", "points")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘doc’
Extract_plant_grapevine_function: no visible global function definition
  for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
File ‘prototest/libs/prototest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘proDA’
Running examples in ‘protti-Ex.R’ failed
The error most likely occurred in:

> ### Name: qc_sample_correlation
> ### Title: Correlation based hirachical clustering of samples
> ### Aliases: qc_sample_correlation
> 
> ### ** Examples
> 
> set.seed(123) # Makes example reproducible
> 
> # Create example data
> data <- create_synthetic_data(
+   n_proteins = 100,
+   frac_change = 0.05,
+   n_replicates = 3,
+   n_conditions = 2,
+   method = "effect_random"
+ )
> 
> # Create sample correlation heatmap
> qc_sample_correlation(
+   data = data,
+   sample = sample,
+   grouping = peptide,
+   intensity_log2 = peptide_intensity_missing,
+   condition = condition
+ )
Error in ser_permutation_vector(order, method = method$name) : 
  'list' object cannot be coerced to type 'integer'
Calls: qc_sample_correlation ... seriate.dist -> ser_permutation -> ser_permutation_vector
Execution halted
Running ‘testthat.R’ [88s/105s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(protti)
  👩🏽‍🔬 Welcome to protti version 0.2.0! 👨🏼‍💻
                              
  🔬 Have fun analysing your data! 💻
  > 
  > test_check("protti")
  $`1`
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-qc_functions.R:119:3): qc_sample_correlation works ──────────────
  Error in `ser_permutation_vector(order, method = method$name)`: 'list' object cannot be coerced to type 'integer'
  Backtrace:
      █
   1. └─protti::qc_sample_correlation(...) test-qc_functions.R:119:2
   2.   └─dendextend::seriate_dendrogram(dendrogram, distance, method = "OLO")
   3.     ├─seriation::seriate(...)
   4.     └─seriation:::seriate.dist(...)
   5.       ├─seriation::ser_permutation(ser_permutation_vector(order, method = method$name))
   6.       └─seriation::ser_permutation_vector(order, method = method$name)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 120 ]
  Error: Test failures
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.7Mb
Undeclared package ‘XML’ in Rd xrefs
Note: found 12717 marked UTF-8 strings
Package suggested but not available for checking: ‘rdt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rdt’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rdt’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rdt’
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.
Note: found 1 marked UTF-8 string
Package in Depends field not imported from: ‘rpart’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘PSAgraphics-Ex.R’ failed
The error most likely occurred in:

> ### Name: loess.psa
> ### Title: Graphic for data and loess-based estimate of effect size after
> ###   propensity score adjustment
> ### Aliases: loess.psa
> ### Keywords: hplot
> 
> ### ** Examples
> 
> #Artificial example where ATE should be 1 over all of (0,1).
> response1 <- c(rep(1, 100), rep(2, 100), rep(3, 100)) + rnorm(300, 0, .5)
> response0 <- c(rep(0, 100), rep(1, 100), rep(2, 100)) + rnorm(300, 0, .5)
> response <- c(response1, response0)
> treatment <- c(rep(1, 300), rep(0, 300))
> propensity <- rep(seq(.01, .99, (.98/299)), 2)
> a <- data.frame(response, treatment, propensity)
> loess.psa(a, span = .15, degree = 1, int = c(0, .33, .67, 1))
Error in data.frame(response, treatment, propensity) : 
  arguments imply differing number of rows: 600, 0
Calls: loess.psa -> data.frame
Execution halted
Namespaces in Imports field not imported from:
  ‘matrixcalc’ ‘tidyr’ ‘utils’
  All declared Imports should be used.
mahalanobisComposite: no visible global function definition for
  ‘princomp’
prepareComposite: no visible global function definition for ‘cov’
winsorizor : f: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  cov princomp quantile
Consider adding
  importFrom("stats", "cov", "princomp", "quantile")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘miceadds’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forecast’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
Note: found 26 marked Latin-1 strings
'library' or 'require' call to ‘numDeriv’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
test.problem : g: no visible global function definition for ‘grad’
test.problem: no visible global function definition for ‘new’
psoptim,test.problem-missing-missing-missing-missing: no visible global
  function definition for ‘new’
show,test.result: no visible global function definition for ‘show’
show,test.result: no visible global function definition for ‘sd’
Undefined global functions or variables:
  grad new sd show
Consider adding
  importFrom("methods", "new", "show")
  importFrom("stats", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
pspearman: no visible global function definition for ‘pt’
spearman.test: no visible global function definition for
  ‘complete.cases’
spearman.test: no visible global function definition for ‘cor’
Undefined global functions or variables:
  complete.cases cor pt
Consider adding
  importFrom("stats", "complete.cases", "cor", "pt")
to your NAMESPACE file.
File ‘pspearman/libs/pspearman.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Non-standard file/directory found at top level:
  ‘orig’
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 43.6Mb
  sub-directories of 1Mb or more:
    libs  42.9Mb
GNU make is a SystemRequirements.
Undeclared package ‘entropy’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘EffectsRelBaseline’ ‘boot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
catEffectBootAdaptor: no visible binding for global variable ‘sumSqCat’
compExclusionFraction: no visible global function definition for
  ‘rpois’
compExclusionFraction: no visible global function definition for
  ‘t.test’
compExclusionFraction: no visible global function definition for ‘glm’
compExclusionFraction: no visible global function definition for
  ‘anova’
compPowerCatSelectivity: no visible binding for global variable
  ‘fRatioStat’
compPowerGeneralRespDetection: no visible binding for global variable
  ‘sumSqCat’
compPowerRespDetection: no visible binding for global variable
  ‘sumSqCat’
compRejectionFraction: no visible global function definition for
  ‘rpois’
compRejectionFraction: no visible global function definition for
  ‘t.test’
compRejectionFraction: no visible global function definition for ‘glm’
compRejectionFraction: no visible global function definition for
  ‘anova’
simCatResp: no visible global function definition for ‘rpois’
simNormCatResp: no visible global function definition for ‘rnorm’
testCatEffectBoot: no visible global function definition for ‘boot’
Undefined global functions or variables:
  anova boot fRatioStat glm rnorm rpois sumSqCat t.test
Consider adding
  importFrom("stats", "anova", "glm", "rnorm", "rpois", "t.test")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘multilevel’ ‘nlme’
A package should be listed in only one of these fields.
Non-standard file/directory found at top level:
  ‘README.txt’
'library' or 'require' calls to packages already attached by Depends:
  ‘multilevel’ ‘nlme’
  Please remove these calls from your code.
installed size is 35.8Mb
  sub-directories of 1Mb or more:
    libs  34.7Mb
Running examples in ‘psych-Ex.R’ failed
The error most likely occurred in:

> ### Name: error.crosses
> ### Title: Plot x and y error bars
> ### Aliases: error.crosses
> ### Keywords: multivariate hplot
> 
> ### ** Examples
> 
> 
> #just draw one pair of variables
> desc <- describe(attitude)
> x <- desc[1,]
> y <- desc[2,]
> error.crosses(x,y,xlab=rownames(x),ylab=rownames(y))   
Warning in max(x$se, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(y$se, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'xlim' values
Calls: error.crosses -> plot -> plot.default -> localWindow -> plot.window
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Namespaces in Imports field not imported from:
  ‘lifecycle’ ‘patchwork’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Note: found 93 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘yaml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
File ‘ptest/libs/ptest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

> ### Name: Change Log
> ### Title: Changes Made to the Package
> ### Aliases: Changes
> ### Keywords: documentation
> 
> ### ** Examples
> 
> #    SRM: magnitude is iid exponential with bvalue=1
> #    simulate and calculate the log-likelihood
> 
> TT <- c(0, 1000)
> bvalue <- 1
> params <- c(-1.5, 0.01, 0.8, bvalue*log(10))
> 
> #   --- Old Method ---
> # x <- pp.sim(NULL, params[1:3], srm.cif, TT, seed=5, magn.sim=1)
> # print(pp.LL(x, srm.cif, params[1:3], TT))
> # [1] -601.3941
> 
> #   --- New Method, no mark density ---
> x1 <- mpp(data=NULL,
+           gif=srm_gif,
+           marks=list(NULL, rexp_mark),
+           params=params,
+           gmap=expression(params[1:3]),
+           mmap=expression(params[4]),
+           TT=TT)
> x1 <- simulate(x1, seed=5)
> print(logLik(x1))
Error in FUN(X, Y, ...) : 
  'list' object cannot be coerced to type 'double'
Calls: print -> logLik -> logLik.mpp -> cif -> outer
Execution halted
'LazyData' is specified without a 'data' directory
Note: found 28898 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R          1.1Mb
    doc        4.0Mb
    examples   2.5Mb
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘R.utils’ ‘rmeta’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ChisqTest_expect: no visible global function definition for ‘pchisq’
plot_chase_observed_expected: no visible global function definition for
  ‘meta.MH’
plot_chase_observed_expected: no visible global function definition for
  ‘txtProgressBar’
plot_chase_observed_expected: no visible global function definition for
  ‘setTxtProgressBar’
test.one.treated: no visible global function definition for
  ‘fisher.test’
test_one: no visible global function definition for ‘rbinom’
test_one: no visible global function definition for ‘fisher.test’
Undefined global functions or variables:
  fisher.test meta.MH pchisq rbinom setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "fisher.test", "pchisq", "rbinom")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Package suggested but not available for checking: ‘fulltext’
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘sjPlot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 42.4Mb
  sub-directories of 1Mb or more:
    libs  42.0Mb
Note: found 35 marked UTF-8 strings
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 31.9Mb
  sub-directories of 1Mb or more:
    libs  31.4Mb
Namespaces in Imports field not imported from:
  ‘data.table’ ‘itsadug’ ‘lazyeval’ ‘mgcv’
  All declared Imports should be used.
Undeclared package ‘tibble’ in Rd xrefs
Running examples in ‘PupilPre-Ex.R’ failed
The error most likely occurred in:

> ### Name: clean_artifact
> ### Title: Automatically clean artifacts.
> ### Aliases: clean_artifact
> 
> ### ** Examples
> 
> # Load example data
> data("Pupilex4")
> 
> # Writing log file to temporary folder for the example
> dat <- clean_artifact(Pupilex4, MADWindow = 100, MADConstant = 2,
+                       MADPadding = c(200, 200), MahaConstant = 2,
+                       Method = "Robust", XandY = TRUE, Second = TRUE,
+                       MaxValueRun = 5, NAsAroundRun = c(2,2),
+                       LogFile = paste0(tempdir(),"/ArtifactCleanupLog.rds"))

Running cleanup based on MAD (median absolute deviation) and robust Mahalanobis distance.
Error in FUN(x, aperm(array(STATS, dims[perm]), order(perm)), ...) : 
  non-numeric argument to binary operator
Calls: clean_artifact ... do.grouped_df -> eval_tidy -> .fixartif -> <Anonymous> -> sweep
Execution halted
PurBayes: no visible global function definition for ‘update’
PurBayes: no visible global function definition for ‘sd’
plot.PurBayes: no visible global function definition for ‘quantile’
plot.PurBayes: no visible global function definition for ‘lines’
summary.PurBayes : <anonymous>: no visible global function definition
  for ‘quantile’
Undefined global functions or variables:
  lines quantile sd update
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "quantile", "sd", "update")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘vctrs’, ‘httr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘readr’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
CandidateBio.getBio : <anonymous>: no visible global function
  definition for ‘na.omit’
Committee.getCommittee : <anonymous>: no visible global function
  definition for ‘na.omit’
getAllBios: no visible global function definition for ‘txtProgressBar’
getAllBios: no visible global function definition for
  ‘setTxtProgressBar’
getAllLocalOfficials: no visible global function definition for
  ‘txtProgressBar’
getAllLocalOfficials: no visible global function definition for
  ‘setTxtProgressBar’
getAllVotes: no visible global function definition for ‘txtProgressBar’
getAllVotes: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  na.omit setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
File ‘PWD/libs/PWD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
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.
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
'LazyData' is specified without a 'data' directory
.grid.matrix: no visible global function definition for ‘slot’
.matrix2grid: no visible global function definition for ‘as’
.poly2grid: no visible global function definition for ‘is’
.poly2grid: no visible global function definition for ‘slot’
.poly2grid: no visible global function definition for ‘as’
.pycno.core : smooth2D : s1d: no visible global function definition for
  ‘filter’
.pycno.core: no visible global function definition for ‘flush.console’
.pycno2matrix: no visible global function definition for ‘slot’
Undefined global functions or variables:
  as filter flush.console is slot
Consider adding
  importFrom("methods", "as", "is", "slot")
  importFrom("stats", "filter")
  importFrom("utils", "flush.console")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘exampleplot_1_blockdist_1.png’ ‘exampleplot_1_blockdist_2.png’
  ‘exampleplot_1_blockdist_3.png’ ‘exampleplot_1_bootdist.png’
  ‘exampleplot_1_dist.png’ ‘exampleplot_1_histogramtest_EMD.png’
  ‘exampleplot_1_roc_dynamic.png’ ‘exampleplot_1_slidedist_1.png’
  ‘exampleplot_1_slidedist_2.png’ ‘exampleplot_1_slidedist_3.png’
  ‘exampleplot_1_trimmeddist.png’ ‘exampleplot_blockdist_1.png’
  ‘exampleplot_blockdist_2.png’ ‘exampleplot_blockdist_3.png’
  ‘exampleplot_bootdist.png’ ‘exampleplot_dist.png’
  ‘exampleplot_lim_dyn.png’ ‘exampleplot_lim_sig.png’
  ‘exampleplot_lim_sta.png’ ‘exampleplot_noc.png’
  ‘exampleplot_roc_dyn.png’ ‘exampleplot_roc_sta.png’
  ‘exampleplot_slidedist_1.png’ ‘exampleplot_slidedist_2.png’
  ‘exampleplot_slidedist_3.png’ ‘exampleplot_trimmeddist.png’
  ‘myworkflow_result.xml’ ‘test_2_roc_dynamic.png’ ‘test_4_dist.png’
  ‘test_5_blockdist_1.png’ ‘test_5_blockdist_2.png’
  ‘test_5_blockdist_3.png’ ‘test_6_slidedist_1.png’
  ‘test_6_slidedist_2.png’ ‘test_6_slidedist_3.png’
  ‘test_7_trimmeddist.png’ ‘test_8_bootdist.png’ ‘test_emd_1d.png’
  ‘test_emd_2d.png’ ‘test_jsd_1d.png’ ‘test_jsd_2d.png’
  ‘test_kld_1d.png’ ‘test_kld_2d.png’ ‘test_ms_1d.png’ ‘test_ms_2d.png’
  ‘test_rms_1d.png’ ‘test_rms_2d.png’
Undeclared package ‘HURDAT’ in Rd xrefs
Unknown package ‘HURDAT’ in Rd xrefs
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Running examples in ‘QCAcluster-Ex.R’ failed
The error most likely occurred in:

> ### Name: partition_min
> ### Title: Generation of conservative or parsimonious solution for
> ###   individual partitions
> ### Aliases: partition_min
> 
> ### ** Examples
> 
> # loading data from Thiem (EPSR, 2011; see data documentation)
> data(Thiem2011)
> 
> # running function for parsimonious solution
> Thiem_pars <- partition_min(
+   dataset = Thiem2011,
+   units = "country", time = "year",
+   cond = c("fedismfs", "homogtyfs", "powdifffs", "comptvnsfs", "pubsupfs", "ecodpcefs"),
+   out = "memberfs",
+   n_cut = 1, incl_cut = 0.8,
+   solution = "P",
+   BE_cons = c(0.9, 0.8, 0.7, 0.8, 0.6, 0.8, 0.8, 0.8, 0.8, 0.8, 0.8),
+   WI_cons = c(0.5, 0.8, 0.7, 0.8, 0.6, rep(0.8, 10)))
Error: Input vectors should be numeric or logical.

Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Aggregation-over-partitions.Rmd’ using rmarkdown
Quitting from lines 38-52 (Aggregation-over-partitions.Rmd) 
Error: processing vignette 'Aggregation-over-partitions.Rmd' failed with diagnostics:
Input vectors should be numeric or logical.


--- failed re-building ‘Aggregation-over-partitions.Rmd’

--- re-building ‘Diversity-of-partitions.Rmd’ using rmarkdown
--- finished re-building ‘Diversity-of-partitions.Rmd’

--- re-building ‘Minimization-of-partitions.Rmd’ using rmarkdown
Quitting from lines 41-57 (Minimization-of-partitions.Rmd) 
Error: processing vignette 'Minimization-of-partitions.Rmd' failed with diagnostics:
Input vectors should be numeric or logical.


--- failed re-building ‘Minimization-of-partitions.Rmd’

--- re-building ‘Weight-of-partitions.Rmd’ using rmarkdown
Quitting from lines 35-47 (Weight-of-partitions.Rmd) 
Error: processing vignette 'Weight-of-partitions.Rmd' failed with diagnostics:
Input vectors should be numeric or logical.


--- failed re-building ‘Weight-of-partitions.Rmd’

SUMMARY: processing the following files failed:
  ‘Aggregation-over-partitions.Rmd’ ‘Minimization-of-partitions.Rmd’
  ‘Weight-of-partitions.Rmd’

Error: Vignette re-building failed.
Execution halted
csQCAbinTest: no visible global function definition for ‘p.adjust’
fsQCApermTest: no visible global function definition for ‘p.adjust’
mvQCAbinTest: no visible global function definition for ‘p.adjust’
p.threshold.adjust: no visible global function definition for
  ‘p.adjust’
plot.fsQCApt: no visible global function definition for ‘dev.cur’
plot.fsQCApt: no visible global function definition for ‘dev.new’
plot.fsQCApt: no visible global function definition for ‘par’
plot.fsQCApt: no visible global function definition for ‘density’
plot.fsQCApt: no visible global function definition for ‘axis’
plot.fsQCApt: no visible global function definition for ‘polygon’
plot.fsQCApt: no visible global function definition for ‘points’
plot.fsQCApt: no visible global function definition for ‘hist’
summary.csQCAbt: no visible global function definition for
  ‘printCoefmat’
summary.fsQCApt: no visible global function definition for
  ‘printCoefmat’
summary.mvQCAbt: no visible global function definition for
  ‘printCoefmat’
Undefined global functions or variables:
  axis density dev.cur dev.new hist p.adjust par points polygon
  printCoefmat
Consider adding
  importFrom("grDevices", "dev.cur", "dev.new")
  importFrom("graphics", "axis", "hist", "par", "points", "polygon")
  importFrom("stats", "density", "p.adjust", "printCoefmat")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    gui          1.7Mb
    libs         2.8Mb
    staticdocs   3.4Mb
Running examples in ‘QCA-Ex.R’ failed
The error most likely occurred in:

> ### Name: XYplot
> ### Title: Create an XY plot
> ### Aliases: XYplot
> ### Keywords: functions
> 
> ### ** Examples
> 
> 
> # Cebotari & Vink (2013)
> # necessity relation between NATPRIDE and PROTEST
> XYplot(CVF[, 5:6])

Error: Input vectors should be numeric or logical.

Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘QCEWAS-Ex.R’ failed
The error most likely occurred in:

> ### Name: EWAS_QC
> ### Title: Automated Quality Control of EWAS results files
> ### Aliases: EWAS_QC
> 
> ### ** Examples
> 
> # For use in this example, the 2 sample files in the
> # extdata folder of the QCEWAS library will be copied
> # to your current R working directory. Running the QC
> # generates 7 new files in your working directory:
> # a cleaned, post-QC dataset, a log file, and 5 graphs.
> # Consult the Quick-Start guide for more information on
> # how to interpret these.
> 
> file.copy(from = file.path(system.file("extdata", package = "QCEWAS"),
+                            "sample_map.txt.gz"),
+           to = getwd(), overwrite = FALSE, recursive = FALSE)
[1] TRUE
> file.copy(from = file.path(system.file("extdata", package = "QCEWAS"),
+                            "sample1.txt.gz"),
+           to = getwd(), overwrite = FALSE, recursive = FALSE)
[1] TRUE
> 
> QC_results <- EWAS_QC(data = "sample1.txt.gz",
+                       map = "sample_map.txt.gz",
+                       outputname = "sample_output",
+                       threshold_outliers = c(-20, 20),
+                       exclude_outliers = FALSE,
+                       exclude_X = TRUE, exclude_Y = FALSE,
+                       save_final_dataset = TRUE, gzip_final_dataset = FALSE)
[1] 
[1]  *** QC'ing sample_output
[1] 
[1] 0 entries with missing values
[1] 0 X-chromosome probes excluded
[1] 309 outliers found
Warning in EWAS_plots(dataset = if (use_map) temp_map else data$P_VAL, plot_QQ = TRUE,  :
  Cannot create a Manhattan plot without chromosome/position values
Error in EWAS_plots(dataset = if (use_map) temp_map else data$P_VAL, plot_QQ = TRUE,  : 
  Missing columns: P_VAL
Calls: EWAS_QC -> EWAS_plots
Execution halted
Found the following files/directories:
  ‘sample1.txt.gz’ ‘sample_map.txt.gz’ ‘sample_output.graph_p.png’
  ‘sample_output.histo.png’
Malformed Description field: should contain one or more complete sentences.
Running examples in ‘QCGWAS-Ex.R’ failed
The error most likely occurred in:

> ### Name: QC_histogram
> ### Title: Histogram(s) of expected and observed data distribution
> ### Aliases: QC_histogram histogram_series
> ### Keywords: distribution
> 
> ### ** Examples
> 
>   data("gwa_sample")
> 
>   QC_histogram(dataset = gwa_sample, data_col = "EFFECT",
+              save_name = "sample_histogram",
+              filter_FRQ = 0.01, filter_cal = 0.95,
+              filter_NA = FALSE,
+              graph_name = "Effect size histogram")
Error in QC_histogram(dataset = gwa_sample, data_col = "EFFECT", save_name = "sample_histogram",  : 
  Insufficient data to apply filters: dataset is single column!
Execution halted
'LazyData' is specified without a 'data' directory
Undeclared package ‘qdap’ in Rd xrefs
Undeclared package ‘gplots’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is 53.6Mb
  sub-directories of 1Mb or more:
    libs  53.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rmarkdown’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 76102 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
chooseMDoubleBootstrap: no visible global function definition for
  ‘model.matrix’
chooseMDoubleBootstrap: no visible global function definition for
  ‘as.formula’
chooseMDoubleBootstrap: no visible global function definition for
  ‘model.frame’
chooseMDoubleBootstrap: no visible global function definition for ‘lm’
chooseMDoubleBootstrap: no visible global function definition for
  ‘coef’
chooseMDoubleBootstrap: no visible global function definition for
  ‘quantile’
chooseMDoubleBootstrap: no visible global function definition for
  ‘qnorm’
getModel: no visible global function definition for ‘lm’
getModel: no visible global function definition for ‘model.matrix’
getModel: no visible global function definition for ‘as.formula’
getModel: no visible global function definition for ‘model.frame’
getModel: no visible global function definition for ‘model.response’
getModel: no visible global function definition for ‘coef’
getModel: no visible global function definition for ‘qnorm’
qLearn: no visible global function definition for ‘model.matrix’
qLearn: no visible global function definition for ‘as.formula’
qLearn: no visible global function definition for ‘model.frame’
qLearn: no visible global function definition for ‘coef’
qLearn: no visible global function definition for ‘lm’
qLearn: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  as.formula coef lm model.frame model.matrix model.response qnorm
  quantile
Consider adding
  importFrom("stats", "as.formula", "coef", "lm", "model.frame",
             "model.matrix", "model.response", "qnorm", "quantile")
to your NAMESPACE file.
installed size is 77.4Mb
  sub-directories of 1Mb or more:
    libs  77.1Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
pcAxisCubeMake: no visible global function definition for ‘aggregate’
pcAxisCubeToCSV: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  aggregate write.csv
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘datInSFexample6_1pxCube.csv’ ‘datInSFexample6_1pxCubeA0.csv ’
  ‘datInSFexample6_1pxCubeA1.csv ’ ‘datInSFexample6_1pxCubeData.csv ’
  ‘datInSFexample6_1pxCubeVariable.csv’
  ‘datInSFexample6_1pxCubeVariableDomain.csv’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Namespaces in Imports field not imported from:
  ‘distr’ ‘ggplot2’
  All declared Imports should be used.
Found the following files/directories:
  ‘lambda.pdf’ ‘qqplot.pdf’
Note: found 7 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
Undeclared package ‘qrNLMM’ in Rd xrefs
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data  10.8Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Note: found 6 marked UTF-8 strings
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘msm’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘purrr’
  All declared Imports should be used.
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
'LazyData' is specified without a 'data' directory
installed size is 43.7Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs     39.0Mb
Malformed Description field: should contain one or more complete sentences.
ci.length: no visible global function definition for ‘qexp’
detectable.bc: no visible global function definition for ‘uniroot’
detectable.f2: no visible global function definition for ‘uniroot’
detectable.ri: no visible global function definition for ‘uniroot’
nu: no visible global function definition for ‘pnorm’
nullinfo: no visible global function definition for ‘qnorm’
nullinfo: no visible global function definition for ‘dnorm’
optselection.bc: no visible global function definition for ‘optimize’
optselection.f2: no visible global function definition for ‘optimize’
optspacing.bc: no visible global function definition for ‘optim’
optspacing.bc: no visible global function definition for ‘optimize’
optspacing.f2: no visible global function definition for ‘optim’
optspacing.f2: no visible global function definition for ‘optimize’
powercalc.bc: no visible global function definition for ‘pchisq’
powercalc.f2: no visible global function definition for ‘pchisq’
samplesize.bc: no visible global function definition for ‘uniroot’
samplesize.f2: no visible global function definition for ‘uniroot’
samplesize.ri: no visible global function definition for ‘uniroot’
tailprob: no visible global function definition for ‘pchisq’
thresh: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  dnorm optim optimize pchisq pnorm qexp qnorm uniroot
Consider adding
  importFrom("stats", "dnorm", "optim", "optimize", "pchisq", "pnorm",
             "qexp", "qnorm", "uniroot")
to your NAMESPACE file.
Undeclared package ‘qtl’ in Rd xrefs
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.8Mb
    doc       3.0Mb
    libs      1.6Mb
Namespace in Imports field not imported from: ‘MatrixModels’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘Rmpfr’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
adjacencyMatrix: no visible global function definition for ‘as’
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘QuACN/libs/QuACN.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘viridis’
  All declared Imports should be used.
Undeclared package ‘rgl’ in Rd xrefs
'LazyData' is specified without a 'data' directory
quadp: no visible global function definition for ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   6.7Mb
alphaf: no visible global function definition for ‘pchisq’
alphaf: no visible global function definition for ‘dbinom’
conout: no visible global function definition for ‘sd’
ibgaout: no visible global function definition for ‘qnorm’
ibgaout: no visible global function definition for ‘pnorm’
plot.qualint: no visible global function definition for ‘qnorm’
powerval: no visible global function definition for ‘rnorm’
powerval: no visible global function definition for ‘qnorm’
powerval: no visible global function definition for ‘pnorm’
print.expplot: no visible global function definition for ‘gray’
print.expplot: no visible binding for global variable ‘coef’
print.outplot: no visible global function definition for ‘gray’
print.outplot: no visible binding for global variable ‘coef’
qualint: no visible global function definition for ‘qnorm’
qualval: no visible global function definition for ‘qnorm’
surout: no visible global function definition for ‘tail’
surout: no visible global function definition for ‘coef’
Undefined global functions or variables:
  coef dbinom gray pchisq pnorm qnorm rnorm sd tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("stats", "coef", "dbinom", "pchisq", "pnorm", "qnorm",
             "rnorm", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Note: found 4 marked UTF-8 strings
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   5.9Mb
Note: found 35707 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘SparseM’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Non-standard file/directory found at top level:
  ‘README.txt’
Rd file 'graph.mod.Rd':
  \usage lines wider than 90 characters:
     graph.mod(ssmod, x, y, data, title = "", xlab = "Centered X", ylab = "Raw Y", ylimit = 1.5, ...)

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘Judge.pdf’
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   4.3Mb
Note: found 4145 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘psych’ ‘psychTools’
  All declared Imports should be used.
Undeclared package ‘reshape’ in Rd xrefs
Running examples in ‘quickblock-Ex.R’ failed
The error most likely occurred in:

> ### Name: quickblock
> ### Title: Construct threshold blockings
> ### Aliases: quickblock
> 
> ### ** Examples
> 
> # Construct example data
> my_data <- data.frame(x1 = runif(100),
+                       x2 = runif(100))
> 
> # Make distances
> my_distances <- distances(my_data, dist_variables = c("x1", "x2"))
Error in distances(data = my_data, dist_variables = c("x1", "x2")) : 
  `dist_variables` must be NULL when `data` is matrix or vector.
Calls: distances -> coerce_distance_data -> new_error
Execution halted
Running ‘testthat.R’ [19s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(quickblock)
  Loading required package: distances
  Please cite the `quickblock` package as:
     Higgins, Michael J., Fredrik Savje and Jasjeet S. Sekhon (2016),
     "Improving massive experiments with threshold blocking",
     Proceedings of the National Academy of Sciences 113:27, 7369--7376.
  > 
  > test_check("quickblock")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_estimator.R:189:3): (code run outside of `test_that()`) ─────────
  <error/condition>
  Error in `distances(data = df)`: `data` must be numeric.
  Backtrace:
      █
   1. ├─quickblock::quickblock(distances(df), size_constraint = 4L) test_estimator.R:189:2
   2. │ └─distances::is.distances(distances)
   3. └─distances::distances(df)
   4.   └─distances:::coerce_distance_data(data, id_variable, dist_variables)
   5.     └─distances:::new_error("`", match.call()$data, "` must be numeric.")
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 242 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running examples in ‘quickmatch-Ex.R’ failed
The error most likely occurred in:

> ### Name: covariate_averages
> ### Title: Covariate averages in matched sample
> ### Aliases: covariate_averages
> 
> ### ** Examples
> 
> # Construct example data
> my_data <- data.frame(y = rnorm(100),
+                       x1 = runif(100),
+                       x2 = runif(100),
+                       treatment = factor(sample(rep(c("T1", "T2", "C"), c(25, 25, 50)))))
> 
> # Make distances
> my_distances <- distances(my_data, dist_variables = c("x1", "x2"))
Error in distances(data = my_data, dist_variables = c("x1", "x2")) : 
  `dist_variables` must be NULL when `data` is matrix or vector.
Calls: distances -> coerce_distance_data -> new_error
Execution halted
Running ‘testthat.R’ [7s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(quickmatch)
  Loading required package: distances
  Please cite the `quickmatch` package as:
     Savje, Fredrik, Michael J. Higgins and Jasjeet S. Sekhon (2017),
     "Generalized Full Matching", arXiv 1703.03882.
     https://arxiv.org/abs/1703.03882
  > 
  > test_check("quickmatch")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_lm_match.R:205:1): (code run outside of `test_that()`) ──────────
  <error/condition>
  Error in `distances(data = df1[c("x1", "x2")])`: `data` must be numeric.
  Backtrace:
      █
   1. ├─quickmatch::quickmatch(distances(df1[c("x1", "x2")]), df1$treat1) test_lm_match.R:205:0
   2. │ └─distances::is.distances(distances)
   3. └─distances::distances(df1[c("x1", "x2")])
   4.   └─distances:::coerce_distance_data(data, id_variable, dist_variables)
   5.     └─distances:::new_error("`", match.call()$data, "` must be numeric.")
  ── Error (test_quickmatch.R:237:1): (code run outside of `test_that()`) ────────
  <error/condition>
  Error in `distances(data = my_data, dist_variables = c("x1", "x2"))`: `dist_variables` must be NULL when `data` is matrix or vector.
  Backtrace:
      █
   1. └─distances::distances(my_data, dist_variables = c("x1", "x2")) test_quickmatch.R:237:0
   2.   └─distances:::coerce_distance_data(data, id_variable, dist_variables)
   3.     └─distances:::new_error(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 478 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
Package suggested but not available for checking: ‘fastshp’
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
Undeclared package ‘PredictABEL’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 99 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘gridExtra’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 12928 marked UTF-8 strings
mutualCoherence : .setOneMutualP: no visible global function definition
  for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Note: found 89912 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘pracma’ ‘zoo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘fields’ in Rd xrefs
Package suggested but not available for checking: ‘ReGenesees’
conf2d.default: no visible global function definition for ‘polygon’
conf2d_int: no visible global function definition for ‘contourLines’
Undefined global functions or variables:
  contourLines polygon
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "polygon")
to your NAMESPACE file.
Undeclared package ‘gplots’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 34 marked UTF-8 strings
'library' or 'require' call to ‘rgdal’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘matrixStats’ ‘rgdal’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following files/directories:
  ‘ndvi.rgf’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lmerTest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘output.html’
Undeclared package ‘generics’ in Rd xrefs
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 32 marked UTF-8 strings
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘rgl’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘lattice’ ‘leaps’ ‘rgl’ ‘s20x’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘collections’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘asd’ ‘cubature’ ‘data.table’ ‘ggplot2’ ‘multxpert’ ‘survival’
  All declared Imports should be used.
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    5.8Mb
    libs   1.0Mb
Namespaces in Imports field not imported from:
  ‘comat’ ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘car’ ‘dplyr’ ‘grid’ ‘gridExtra’ ‘knitr’ ‘lmerTest’ ‘tidyr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
getsonde: no visible global function definition for ‘read.table’
plotsonde: no visible global function definition for ‘par’
plotwind: no visible global function definition for ‘mtext’
plotwind: no visible global function definition for ‘abline’
skewt.axis: no visible global function definition for ‘par’
skewt.axis: no visible global function definition for ‘axis’
skewt.axis: no visible global function definition for ‘mtext’
skewt.axis: no visible global function definition for ‘segments’
skewt.axis: no visible global function definition for ‘text’
skewt.axis: no visible global function definition for ‘lines’
skewt.lines: no visible global function definition for ‘lines’
skewt.points: no visible global function definition for ‘points’
station.symbol: no visible global function definition for ‘sd’
station.symbol: no visible global function definition for ‘par’
station.symbol: no visible global function definition for ‘lines’
station.symbol: no visible global function definition for ‘polygon’
station.symbol: no visible global function definition for ‘text’
station.symbol: no visible global function definition for ‘segments’
Undefined global functions or variables:
  abline axis lines mtext par points polygon read.table sd segments
  text
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "par",
             "points", "polygon", "segments", "text")
  importFrom("stats", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘SondeFile.txt’
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.4Mb
Malformed Description field: should contain one or more complete sentences.
Rd file 'MDMnMod.Rd':
  \usage lines wider than 90 characters:
     MDMnMod(MDMn.form, data, ID, dist="MDMn", scale.covar=FALSE, est.var=TRUE, calc.resid=TRUE, trace=TRUE)
  \examples lines wider than 100 characters:
     model.nij <- MDMnMod(nij.form, data=n.data, ID=n.data$i, dist="MDMn", scale.covar=TRUE, est.var=FALSE, calc.resid=TRUE, trace=TRUE)

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘utf8’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
RnDif.het: no visible global function definition for ‘runif’
RnDif.hom: no visible global function definition for ‘runif’
RnDifAdv.hom: no visible global function definition for ‘runif’
SoilAdv.hom: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcompadre’
  All declared Imports should be used.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘CGHbase’
  All declared Imports should be used.
Undeclared packages ‘longitudinal’, ‘gRbase’ in Rd xrefs
Error(s) in re-building vignettes:
--- re-building ‘rainbow.Rnw’ using Sweave
Loading required package: MASS
Loading required package: pcaPP
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    libs  25.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets        9.8Mb
    super-tiny-icons   1.0Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    api           3.2Mb
    htmlwidgets   7.1Mb
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘stringi’ ‘xml2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘blcs.dot’ ‘blcs.pdf’ ‘ex1.dot’ ‘ex1.pdf’ ‘ex1bridge1.dot’
  ‘ex1bridge1.pdf’ ‘ex1bridge2.dot’ ‘ex1bridge2.pdf’ ‘ex1bridge3.dot’
  ‘ex1bridge3.pdf’ ‘ex1effect1.dot’ ‘ex1effect1.pdf’ ‘ex1effect2.dot’
  ‘ex1effect2.pdf’ ‘gcmlinear.dot’ ‘gcmlinear.pdf’ ‘latent.dot’
  ‘latent.pdf’ ‘lcs.dot’ ‘lcs.pdf’ ‘mimic.dot’ ‘mimic.pdf’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Non-standard file/directory found at top level:
  ‘COPYRIGHTS’
Copyright information should be in file inst/COPYRIGHTS
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.2Mb
    libs   5.4Mb
Running examples in ‘RandomFields-Ex.R’ failed
The error most likely occurred in:

> ### Name: RFboxcox
> ### Title: Linear part of 'RMmodel'
> ### Aliases: RFboxcox
> ### Keywords: spatial
> 
> ### ** Examples
> ## Don't show: 
> StartExample()
> ## End(Don't show)
> RFoptions(seed=0) ## *ANY* simulation will have the random seed 0; set
> ##                   RFoptions(seed=NA) to make them all random again
> 
> data(soil)
> str(soil)
'data.frame':	201 obs. of  9 variables:
 $ x.coord : num  -90 -60 -30 0 30 60 90 -120 -90 -60 ...
 $ y.coord : num  -150 -150 -150 -150 -150 -150 -150 -120 -120 -120 ...
 $ nr      : int  1 2 3 4 5 6 7 8 9 10 ...
 $ moisture: num  7.23 14.63 12.67 13.73 7.4 ...
 $ NO3.N   : num  3.77 7.83 11.49 14.48 5.67 ...
 $ Total.N : num  34.5 44.2 50.6 52.2 42.2 ...
 $ NH4.N   : num  4.46 5.14 7.28 6.45 3.45 ...
 $ DOC     : num  107 135 152 136 135 ...
 $ N20N    : num  0.000496 0.000404 0.00031 0.000461 0.000518 ...
> soil <- RFspatialPointsDataFrame(
+  coords = soil[ , c("x.coord", "y.coord")],
+  data = soil[ , c("moisture", "NO3.N", "Total.N", "NH4.N", "DOC", "N20N")],
+  RFparams=list(vdim=6, n=1)
+ )
Error in validObject(.Object) : 
  invalid class “RFpointsDataFrame” object: invalid object for slot "coords" in class "RFpointsDataFrame": got class "data.frame", should be or extend class "matrix"
Calls: RFspatialPointsDataFrame ... RFpointsDataFrame -> new -> initialize -> initialize -> validObject
Execution halted
'LazyData' is specified without a 'data' directory
anovaF: no visible global function definition for ‘anova’
anovaF: no visible global function definition for ‘lm’
randInterval: no visible global function definition for ‘quantile’
randInterval : <anonymous>: no visible global function definition for
  ‘quantile’
randPlot: no visible global function definition for ‘par’
randPlot: no visible global function definition for ‘hist’
randPlot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline anova hist lm par quantile
Consider adding
  importFrom("graphics", "abline", "hist", "par")
  importFrom("stats", "anova", "lm", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘curl’ ‘jsonlite’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
bartels.rank.test: no visible global function definition for ‘na.omit’
bartels.rank.test: no visible global function definition for ‘pbeta’
bartels.rank.test: no visible global function definition for ‘pnorm’
cox.stuart.test: no visible global function definition for ‘pbinom’
difference.sign.test: no visible global function definition for
  ‘na.omit’
difference.sign.test: no visible global function definition for ‘pnorm’
rank.test: no visible global function definition for ‘na.omit’
rank.test: no visible global function definition for ‘pnorm’
rruns: no visible global function definition for ‘runif’
runs.test: no visible global function definition for ‘median’
runs.test: no visible global function definition for ‘na.omit’
runs.test: no visible global function definition for ‘points’
runs.test: no visible global function definition for ‘abline’
runs.test: no visible global function definition for ‘gray’
runs.test: no visible global function definition for ‘pnorm’
turning.point.test: no visible global function definition for ‘embed’
turning.point.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline embed gray median na.omit pbeta pbinom pnorm points runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "points")
  importFrom("stats", "embed", "median", "na.omit", "pbeta", "pbinom",
             "pnorm", "runif")
to your NAMESPACE file.
Running examples in ‘rangeBuilder-Ex.R’ failed
The error most likely occurred in:

> ### Name: coordError
> ### Title: Coordinate error
> ### Aliases: coordError
> 
> ### ** Examples
> 
> data(crotalus)
> 
> xy <- crotalus[1:100, c('decimallongitude','decimallatitude')]
> 
> coordError(xy)
Error in coordError(xy) : coords must be of class numeric or character.
Execution halted
Note: found 7734 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘dplyr’ ‘jsonlite’ ‘rgbif’ ‘rgdal’ ‘rgeos’ ‘sp’ ‘spThin’
  ‘spatstat’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Suggests orphaned package: ‘RGtk2’
Malformed Description field: should contain one or more complete sentences.
rank.L2R: no visible global function definition for ‘kmeans’
rank.L2R: no visible global function definition for ‘pnorm’
rank.LN: no visible global function definition for ‘kmeans’
rank.LN: no visible global function definition for ‘pnorm’
rank.gs: no visible global function definition for ‘qnorm’
rank.wald: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  kmeans pnorm qnorm
Consider adding
  importFrom("stats", "kmeans", "pnorm", "qnorm")
to your NAMESPACE file.
File ‘RANKS/libs/RANKS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RJDBC’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘BSgenome.Hsapiens.UCSC.hg19’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
freq: no visible global function definition for ‘xtabs’
freq: no visible binding for global variable ‘na.pass’
freq: no visible global function definition for ‘melt’
freq: no visible global function definition for ‘complete.cases’
freq: no visible global function definition for ‘tail’
kurtosis: no visible global function definition for ‘na.omit’
label: no visible global function definition for ‘tail’
name: no visible global function definition for ‘tail’
nvalid : <anonymous>: no visible global function definition for
  ‘na.omit’
rp.desc: no visible global function definition for ‘melt.data.frame’
rp.desc: no visible global function definition for ‘cast’
rp.desc: no visible global function definition for ‘na.omit’
rp.desc : <anonymous>: no visible global function definition for ‘tail’
rp.desc : <anonymous>: no visible global function definition for ‘head’
rp.freq: no visible global function definition for ‘xtabs’
rp.freq: no visible binding for global variable ‘na.pass’
rp.freq: no visible global function definition for ‘melt’
rp.freq: no visible global function definition for ‘complete.cases’
rp.freq: no visible global function definition for ‘tail’
rp.label: no visible global function definition for ‘tail’
rp.name: no visible global function definition for ‘tail’
rp.outlier : lundcrit: no visible global function definition for ‘qf’
rp.outlier: no visible global function definition for ‘lm’
rp.outlier: no visible global function definition for ‘rstandard’
rp.valid : <anonymous>: no visible global function definition for
  ‘na.omit’
skewness: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  cast complete.cases head lm melt melt.data.frame na.omit na.pass qf
  rstandard tail xtabs
Consider adding
  importFrom("stats", "complete.cases", "lm", "na.omit", "na.pass", "qf",
             "rstandard", "xtabs")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
fnRAP: no visible global function definition for ‘chisq.test’
fnRAP: no visible global function definition for ‘combn’
Undefined global functions or variables:
  chisq.test combn
Consider adding
  importFrom("stats", "chisq.test")
  importFrom("utils", "combn")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gurobi’
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs  10.2Mb
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Running ‘testthat.R’ [33s/48s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(raptr)
  Loading required package: sp
  Loading required package: raster
  The gorubi software is not installed
  Follow these instructions to download the Gurobi software suite:
     http://bit.ly/1ksXUaQ
  
  The Gurobi R package requires a Gurobi license to work:
    visit this web-page for an overview: http://bit.ly/1OHEQCm
    academics can obtain a license at no cost here: http://bit.ly/1iYg3LX
  
  Follow these instructions to install the "gurobi" R package:
     http://bit.ly/1HLCRoE
  
  
  Type the code "is.GurobiInstalled()" to check if Gurobi is
  succesfully installed after following these instructions.
  > test_check("raptr")
  .....
'LazyData' is specified without a 'data' directory
INT_FIX: no visible global function definition for ‘rbinom’
INT_FIX: no visible global function definition for ‘glm’
INT_FIX: no visible global function definition for ‘as.formula’
INT_FIX: no visible global function definition for ‘residuals’
INT_FIX: no visible global function definition for ‘var’
INT_RAN: no visible global function definition for ‘rbinom’
INT_RAN: no visible global function definition for ‘as.formula’
INT_RAN: no visible global function definition for ‘predict’
JOINT: no visible global function definition for ‘rbinom’
JOINT: no visible global function definition for ‘glm’
JOINT: no visible global function definition for ‘as.formula’
JOINT: no visible global function definition for ‘var’
JOINT: no visible global function definition for ‘residuals’
pKuonen: no visible global function definition for ‘pchisq’
pKuonen: no visible global function definition for ‘uniroot’
pKuonen: no visible global function definition for ‘pnorm’
rareGE: no visible global function definition for ‘rbinom’
rareGE: no visible global function definition for ‘as.formula’
rareGE: no visible global function definition for ‘predict’
rareGE: no visible global function definition for ‘glm’
rareGE: no visible global function definition for ‘residuals’
rareGE: no visible global function definition for ‘var’
rareGE_joint_mc: no visible global function definition for ‘pchisq’
rareGE_joint_mc: no visible global function definition for ‘qchisq’
wuweights: no visible global function definition for ‘dbeta’
Undefined global functions or variables:
  as.formula dbeta glm pchisq pnorm predict qchisq rbinom residuals
  uniroot var
Consider adding
  importFrom("stats", "as.formula", "dbeta", "glm", "pchisq", "pnorm",
             "predict", "qchisq", "rbinom", "residuals", "uniroot",
             "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
BiogTest.individual: no visible global function definition for ‘combn’
BiogTest.individual: no visible global function definition for ‘runif’
BiogTest.individual: no visible global function definition for ‘rlnorm’
BiogTest.individual: no visible global function definition for
  ‘rnbinom’
BiogTest.sample: no visible global function definition for ‘combn’
BiogTest.sample: no visible global function definition for ‘runif’
BiogTest.sample: no visible global function definition for ‘rlnorm’
BiogTest.sample: no visible global function definition for ‘rnbinom’
BiogTest.sample: no visible global function definition for ‘aggregate’
EcoTest.individual: no visible global function definition for ‘xtabs’
plot.BiogTest: no visible global function definition for ‘quantile’
plot.BiogTest: no visible global function definition for ‘combn’
plot.EcoTest: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  aggregate combn quantile rlnorm rnbinom runif xtabs
Consider adding
  importFrom("stats", "aggregate", "quantile", "rlnorm", "rnbinom",
             "runif", "xtabs")
  importFrom("utils", "combn")
to your NAMESPACE file.
Undeclared package ‘arm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
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.
Undeclared package ‘htmlwidgets’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘crosstalk’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
rateratio.test: no visible global function definition for
  ‘complete.cases’
rateratio.test: no visible global function definition for ‘pbinom’
rateratio.test : p.L: no visible global function definition for ‘qbeta’
rateratio.test : p.U: no visible global function definition for ‘qbeta’
Undefined global functions or variables:
  complete.cases pbinom qbeta
Consider adding
  importFrom("stats", "complete.cases", "pbinom", "qbeta")
to your NAMESPACE file.
installed size is 60.4Mb
  sub-directories of 1Mb or more:
    libs  59.6Mb
GNU make is a SystemRequirements.
concordance: no visible global function definition for ‘quantile’
concordance : Normal: no visible global function definition for ‘qnorm’
concordance : Normal: no visible global function definition for ‘pnorm’
concordance : MC: no visible global function definition for ‘rmultinom’
concordance : MC: no visible global function definition for ‘quantile’
concordance: no visible global function definition for ‘qnorm’
concordance: no visible global function definition for ‘pnorm’
concordance : Chisq: no visible global function definition for ‘qchisq’
concordance : Chisq: no visible global function definition for ‘pchisq’
concordance : Normal2: no visible global function definition for
  ‘qnorm’
concordance : Normal2: no visible global function definition for
  ‘pnorm’
concordance : MC2: no visible global function definition for
  ‘rmultinom’
concordance : MC2: no visible global function definition for ‘quantile’
wlin.conc: no visible global function definition for ‘quantile’
wlin.conc : MC: no visible global function definition for ‘rmultinom’
wlin.conc : MC: no visible global function definition for ‘quantile’
wquad.conc: no visible global function definition for ‘quantile’
wquad.conc : MC: no visible global function definition for ‘rmultinom’
wquad.conc : MC: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  pchisq pnorm qchisq qnorm quantile rmultinom
Consider adding
  importFrom("stats", "pchisq", "pnorm", "qchisq", "qnorm", "quantile",
             "rmultinom")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘RDperm.Rnw’ using knitr
Loading required package: RATest
Loading required package: ggplot2
Loading required package: gridExtra
Warning in eval(family$initialize) :
  non-integer #successes in a binomial glm!
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path,  :
  dots in figure paths replaced with _ ("figure/panel_a")
Warning in eval(family$initialize) :
  non-integer #successes in a binomial glm!
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path,  :
  dots in figure paths replaced with _ ("figure/panel_b")
Quitting from lines 713-716 (RDperm.Rnw) 
Error: processing vignette 'RDperm.Rnw' failed with diagnostics:
comparison of these types is not implemented
--- failed re-building ‘RDperm.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
.GCD: no visible global function definition for ‘as.polynomial’
.LCM: no visible global function definition for ‘as.polynomial’
.is_zero_polynomial: no visible global function definition for ‘coef’
.poly2expr: no visible global function definition for ‘coef’
integral.rationalfun: no visible global function definition for ‘coef’
integraterf.transcendent: no visible global function definition for
  ‘coef’
rationalfun: no visible global function definition for ‘polynomial’
rationalfun.poly: no visible global function definition for
  ‘polynomial’
rationalfun.poly: no visible global function definition for
  ‘is.polynomial’
rfun: no visible global function definition for ‘polynomial’
rfun.poly: no visible global function definition for ‘polynomial’
rfun.poly: no visible global function definition for ‘is.polynomial’
simplify: no visible global function definition for ‘coef’
simplify: no visible global function definition for ‘polynomial’
Undefined global functions or variables:
  as.polynomial coef is.polynomial polynomial
Consider adding
  importFrom("stats", "coef")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Running examples in ‘RAT-Ex.R’ failed
The error most likely occurred in:

> ### Name: h.index
> ### Title: H-index.
> ### Aliases: h.index
> 
> ### ** Examples
> 
> id = wos("A-8820-2008")
Downloading data


Parsing XML

At least one of your publications has more than 100 authors listed on it. Parsing the data from these publications will take some time.
At least one of your publications has more than 100 addresses listed on it. Parsing the data from these publications will take some time.
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
RAT
 --- call from context --- 
wos("A-8820-2008")
 --- call from argument --- 
if (class(id) == "try-error") {
    warning("Could not connect to server.")
    return()
} else {
    return(id)
}
 --- R stacktrace ---
where 1: wos("A-8820-2008")

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (id, user = NULL, pass = NULL, coll = c("SCI", "SSCI", 
    "AHCI", "ISTP", "ISSHP", "BSCI", "BHCI", "ESCI")) 
{
    if (!grepl("=", id)) {
        if (grepl("\\d", id)) 
            query = paste("AI =", id)
        else query = paste("AU =", id)
    }
    else {
        query = id
    }
    id = try(wosr::pull_wos(query = query, editions = coll, sid = auth(username = user, 
        password = pass)), silent = TRUE)
    if (class(id) == "try-error") {
        warning("Could not connect to server.")
        return()
    }
    else {
        return(id)
    }
}
<bytecode: 0x4d54940>
<environment: namespace:RAT>
 --- function search by body ---
Function wos in namespace RAT has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(id) == "try-error") { : the condition has length > 1
Calls: wos
Execution halted
Package suggested but not available for checking: ‘rggobi’

Suggests orphaned packages:
  ‘RGtk2’ ‘cairoDevice’
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    etc    1.9Mb
    po     1.2Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs  10.3Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
.avisApiBusAvanzada: no visible global function definition for
  ‘read.csv’
.avisRenderMapAdmin: no visible global function definition for ‘points’
.avisRenderMapAdmin: no visible global function definition for ‘rect’
.avisRenderMapPhysical: no visible global function definition for
  ‘points’
avisMap: no visible global function definition for ‘par’
avisMap: no visible global function definition for ‘layout’
Undefined global functions or variables:
  layout par points read.csv rect
Consider adding
  importFrom("graphics", "layout", "par", "points", "rect")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   3.3Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Note: found 8 marked UTF-8 strings
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  26.9Mb
GNU make is a SystemRequirements.
Undeclared packages ‘MCMCpack’, ‘gtools’ in Rd xrefs
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.
'LazyData' is specified without a 'data' directory
installed size is 40.8Mb
  sub-directories of 1Mb or more:
    libs  40.2Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’ ‘testthat’
  All declared Imports should be used.
GNU make is a SystemRequirements.
GetHistoricTradeData: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-clang/Rblpapi.Rcheck/00install.out’ for details.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    blp    7.1Mb
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Malformed Title field: should not end in a period.
SumTestSens: no visible global function definition for ‘pnorm’
binarysens: no visible global function definition for ‘dbinom’
hlsens: no visible global function definition for ‘wilcox.test’
iv_sens: no visible global function definition for ‘pnorm’
mcontrol: no visible global function definition for ‘pnorm’
psens: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dbinom pnorm wilcox.test
Consider adding
  importFrom("stats", "dbinom", "pnorm", "wilcox.test")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
find_available_versions: no visible global function definition for
  ‘contrib.url’
find_available_versions: no visible global function definition for
  ‘available.packages’
install_version: no visible global function definition for
  ‘contrib.url’
install_version: no visible global function definition for
  ‘available.packages’
install_version: no visible global function definition for
  ‘install_url’
load_available_packages: no visible global function definition for
  ‘contrib.url’
validate_installed_package: no visible global function definition for
  ‘installed.packages’
Undefined global functions or variables:
  available.packages contrib.url install_url installed.packages
Consider adding
  importFrom("utils", "available.packages", "contrib.url",
             "installed.packages")
to your NAMESPACE file.
Note: found 26334 marked UTF-8 strings
Found the following files/directories:
  ‘rcanvec.cache’
RC.read.table: no visible global function definition for ‘type.convert’
Undefined global functions or variables:
  type.convert
Consider adding
  importFrom("utils", "type.convert")
to your NAMESPACE file.
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.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 36.5Mb
  sub-directories of 1Mb or more:
    libs  35.8Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’ ‘shinythemes’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.RData’
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    cont  25.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
.onAttach: no visible global function definition for
  ‘packageDescription’
rselect.list: no visible global function definition for ‘select.list’
Undefined global functions or variables:
  packageDescription select.list
Consider adding
  importFrom("utils", "packageDescription", "select.list")
to your NAMESPACE file.
Found the following files/directories:
  ‘data.csv’
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
get_ClinicalCodes: no visible global function definition for ‘read.csv’
get_ClinicalCodes : <anonymous>: no visible global function definition
  for ‘read.csv’
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
cmaOptimDP: no visible global function definition for ‘flush.console’
Undefined global functions or variables:
  flush.console
Consider adding
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Found the following files/directories:
  ‘outcmaesdisp.dat’
Undeclared package ‘car’ in Rd xrefs
Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
enterTableMHTest : onOK: no visible global function definition for
  ‘na.omit’
startStop: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
'library' or 'require' call to ‘FrF2.catlg128’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Undeclared packages ‘BsMD’, ‘rsm’, ‘AlgDesign’, ‘lhs’ in Rd xrefs
managedata: no visible binding for global variable ‘data’
Undefined global functions or variables:
  data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘car’, ‘leaps’, ‘latticeExtra’, ‘rgl’ in Rd xrefs
'library' or 'require' calls in package code:
  ‘abind’ ‘e1071’ ‘qcc’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
BOXWP: no visible binding for global variable ‘top’
BOXWP: no visible binding for global variable ‘buttonsFrame’
HIST: no visible binding for global variable ‘top’
HIST: no visible binding for global variable ‘buttonsFrame’
QQN: no visible binding for global variable ‘top’
QQN: no visible binding for global variable ‘buttonsFrame’
Undefined global functions or variables:
  buttonsFrame top
fncLRpROC: no visible global function definition for ‘palette’
fncLRpROC : onOK : convert: no visible global function definition for
  ‘col2rgb’
fncLRpROC : onOK : convert: no visible global function definition for
  ‘rgb’
fncPairedpROC: no visible global function definition for ‘palette’
fncPairedpROC : onOK : convert: no visible global function definition
  for ‘col2rgb’
fncPairedpROC : onOK : convert: no visible global function definition
  for ‘rgb’
fncUnpairedpROC: no visible global function definition for ‘palette’
fncUnpairedpROC : onOK : convert: no visible global function definition
  for ‘col2rgb’
fncUnpairedpROC : onOK : convert: no visible global function definition
  for ‘rgb’
fncvpROC: no visible global function definition for ‘palette’
fncvpROC : onOK : convert: no visible global function definition for
  ‘col2rgb’
fncvpROC : onOK : convert: no visible global function definition for
  ‘rgb’
Undefined global functions or variables:
  col2rgb palette rgb
Consider adding
  importFrom("grDevices", "col2rgb", "palette", "rgb")
to your NAMESPACE file.
SampleSizes: no visible global function definition for ‘xtabs’
SampleSizes: no visible global function definition for ‘weighted.mean’
SampleSizes: no visible global function definition for ‘reshape’
stage1Sample.fn: no visible global function definition for ‘runif’
stage2Sample.fn: no visible global function definition for ‘runif’
strata.options : onOK: no visible global function definition for
  ‘packageDescription’
Undefined global functions or variables:
  packageDescription reshape runif weighted.mean xtabs
Consider adding
  importFrom("stats", "reshape", "runif", "weighted.mean", "xtabs")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
'library' or 'require' call to ‘SLC’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘SLC’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rcmdr.steeptestDij : onOK: no visible binding for global variable
  ‘replications’
Rcmdr.steeptestPij : onOK: no visible binding for global variable
  ‘replications’
Undefined global functions or variables:
  replications
Consider adding
  importFrom("stats", "replications")
to your NAMESPACE file.
Undeclared packages ‘e1071’, ‘RcmdrMisc’ in Rd xrefs
Package suggested but not available for checking: ‘ROpenOffice’
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   2.3Mb
    po    2.4Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
brewer.pal: no visible global function definition for ‘rgb’
display.brewer.all: no visible global function definition for ‘par’
display.brewer.all: no visible global function definition for ‘rect’
display.brewer.all: no visible global function definition for ‘text’
display.brewer.pal: no visible global function definition for ‘image’
Undefined global functions or variables:
  image par rect rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "image", "par", "rect", "text")
to your NAMESPACE file.
Note: found 345 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
addLine: no visible global function definition for ‘abline’
ellipse: no visible global function definition for ‘approx’
ellipse: no visible global function definition for ‘tail’
Undefined global functions or variables:
  abline approx tail
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "approx")
  importFrom("utils", "tail")
to your NAMESPACE file.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    corpora   7.6Mb
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      1.6Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Undeclared package ‘RcppExamples’ in Rd xrefs
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    lib    4.5Mb
    libs   1.3Mb
‘cleanup’: /bin/bash is not portable
Error(s) in re-building vignettes:
--- re-building ‘RcppCNPy-intro.Rmd’ using rmarkdown
! LaTeX Error: File `lettrine.sty' not found.

! Emergency stop.
<read *> 

Error: processing vignette 'RcppCNPy-intro.Rmd' failed with diagnostics:
LaTeX failed to compile /data/gannet/ripley/R/packages/tests-clang/RcppCNPy.Rcheck/vign_test/RcppCNPy/vignettes/RcppCNPy-intro.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See RcppCNPy-intro.log for more info.
--- failed re-building ‘RcppCNPy-intro.Rmd’

--- re-building ‘UsingReticulate.Rmd’ using rmarkdown
! LaTeX Error: File `lettrine.sty' not found.

! Emergency stop.
<read *> 

Error: processing vignette 'UsingReticulate.Rmd' failed with diagnostics:
LaTeX failed to compile /data/gannet/ripley/R/packages/tests-clang/RcppCNPy.Rcheck/vign_test/RcppCNPy/vignettes/UsingReticulate.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See UsingReticulate.log for more info.
--- failed re-building ‘UsingReticulate.Rmd’

SUMMARY: processing the following files failed:
  ‘RcppCNPy-intro.Rmd’ ‘UsingReticulate.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
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 31.0Mb
  sub-directories of 1Mb or more:
    include   7.9Mb
    libs     22.4Mb
Gauss: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
File ‘RcppFaddeeva/libs/RcppFaddeeva.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
‘configure’: /bin/bash is not portable
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is 45.8Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib      33.2Mb
    libs     10.4Mb
Output from running autoreconf:
  /usr/local/share/autoconf/autoconf/trailer.m4:4: warning: AC_OUTPUT was never used
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    include   7.0Mb
    libs      2.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    include   2.1Mb
    lib       2.6Mb
GNU make is a SystemRequirements.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.4Mb
    libs      3.7Mb
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 16.7Mb
  sub-directories of 1Mb or more:
    include        1.5Mb
    jsonexamples   3.8Mb
    libs          11.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘inline’ in Rd xrefs
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 ‘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.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Suggests orphaned package: ‘bibtex’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
Undeclared package ‘Rglpk’ in Rd xrefs
'LazyData' is specified without a 'data' directory
distimage: no visible binding for global variable ‘terrain.colors’
distimage: no visible global function definition for ‘filled.contour’
distimage: no visible global function definition for ‘title’
distimage: no visible global function definition for ‘axis’
distimage: no visible global function definition for ‘lines’
drawkpc: no visible global function definition for ‘segments’
drawkpc: no visible global function definition for ‘lines’
modelimage: no visible binding for global variable ‘topo.colors’
modelimage: no visible global function definition for ‘filled.contour’
modelimage: no visible global function definition for ‘title’
modelimage: no visible global function definition for ‘axis’
modelimage: no visible global function definition for ‘lines’
sincdata: no visible global function definition for ‘runif’
sincdata: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  axis filled.contour lines rnorm runif segments terrain.colors title
  topo.colors
Consider adding
  importFrom("grDevices", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "filled.contour", "lines", "segments",
             "title")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
sumry_categorical: no visible global function definition for ‘freq’
sumry_continous: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  freq quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs  17.8Mb
Undeclared package ‘Rtsne’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘synchronicity’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following files/directories:
  ‘a.desc’ ‘b.desc’ ‘barrnumleft.desc’ ‘barrsense.desc’ ‘c.desc’
  ‘m.desc’ ‘u.desc’ ‘x’ ‘x.desc’
ip2coordinates: no visible global function definition for ‘URLencode’
street2coordinates: no visible global function definition for
  ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
Found the following files/directories:
  ‘example.pdf’
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Package suggested but not available for checking: ‘webshot2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘readMzXmlData’, ‘MALDIquantForeign’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.txt’ ‘temp2.csv’ ‘temp3.rda’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘MALDIquantForeign’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared package ‘magrittr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Undeclared packages ‘tidyselect’, ‘vctrs’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked Latin-1 string
  Note: found 1 marked UTF-8 string
  Note: found 7 strings marked as "bytes"
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 8 marked UTF-8 strings
Undeclared package ‘rebus.unicode’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.9Mb
'LazyData' is specified without a 'data' directory
ReCiPa: no visible global function definition for ‘count.fields’
ReCiPa: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  count.fields read.table
Consider adding
  importFrom("utils", "count.fields", "read.table")
to your NAMESPACE file.
Undeclared package ‘hardhat’ in Rd xrefs
Running examples in ‘recipes-Ex.R’ failed
The error most likely occurred in:

> ### Name: step_classdist
> ### Title: Distances to Class Centroids
> ### Aliases: step_classdist
> 
> ### ** Examples
> 
> 
> # in case of missing data...
> mean2 <- function(x) mean(x, na.rm = TRUE)
> 
> # define naming convention
> rec <- recipe(Species ~ ., data = iris) %>%
+   step_classdist(all_numeric_predictors(), class = "Species",
+                  pool = FALSE, mean_func = mean2, prefix = "centroid_")
> 
> # default naming
> rec <- recipe(Species ~ ., data = iris) %>%
+   step_classdist(all_numeric_predictors(), class = "Species",
+                  pool = FALSE, mean_func = mean2)
> 
> rec_dists <- prep(rec, training = iris)
Error in FUN(x, aperm(array(STATS, dims[perm]), order(perm)), ...) : 
  non-numeric argument to binary operator
Calls: prep ... bake.step_classdist -> lapply -> FUN -> mahalanobis -> sweep
Execution halted
Note: found 1036 marked UTF-8 strings
Undeclared package ‘car’ in Rd xrefs
Package suggested but not available for checking: ‘opencv’
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   2.4Mb
Namespaces in Imports field not imported from:
  ‘DBI’ ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Found the following files/directories:
  ‘Filled.RData’ ‘cleaned.RData’ ‘days’ ‘gridded’
'LazyData' is specified without a 'data' directory
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
'LazyData' is specified without a 'data' directory
‘configure’: /bin/bash is not portable
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘SemiPar’ ‘caret’ ‘dplyr’ ‘scales’
  All declared Imports should be used.
Suggests orphaned package: ‘bibtex’
Running examples in ‘refreg-Ex.R’ failed
The error most likely occurred in:

> ### Name: trivRegr
> ### Title: Trivariate regression model
> ### Aliases: trivRegr
> 
> ### ** Examples
> 
> dm_no = subset(aegis,aegis$dm=="no")
> 
> # Model formulas
> mu1 = fpg ~ s(age)
> mu2 = hba1c ~ s(age)
> mu3 = fru~s(age)
> var1 = ~ s(age)
> var2 = ~ s(age)
> var3 = ~s(age)
> theta12 =  ~ s(age)
> theta13 =  ~ s(age)
> theta23 =  ~ s(age)
> f = list(mu1,mu2,mu3,var1,var2,var3,theta12,theta13,theta23)
> 
> # Model fit
> fit = trivRegr(f,data=dm_no)
> # Trivariate region estimation
> region = trivRegion(fit,tau=0.95)
Error in linbin(x, gpoints, truncate) : 
  'list' object cannot be coerced to type 'double'
Calls: trivRegion -> kde -> hpi -> dpik -> linbin
Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘registr’
  All declared Imports should be used.
Running examples in ‘regclass-Ex.R’ failed
The error most likely occurred in:

> ### Name: extrapolation_check
> ### Title: A crude check for extrapolation
> ### Aliases: extrapolation.check extrapolation_check
> 
> ### ** Examples
> 
>   data(SALARY)
>   M <- lm(Salary~Education*Experience+Months,data=SALARY)
>   newdata <- data.frame(Education=c(0,5,10),Experience=c(15,15,15),Months=c(0,0,0))
>   extrapolation_check(M,newdata) 
Error in FUN(x, aperm(array(STATS, dims[perm]), order(perm)), ...) : 
  non-numeric argument to binary operator
Calls: extrapolation_check -> mahalanobis -> sweep
Execution halted
Malformed Title field: should not end in a period.
cluster.reg: no visible global function definition for ‘rnorm’
cluster.reg: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘EnvironmentalA.txt’ ‘EnvironmentalB.txt’ ‘Example.txt’
  ‘Example_Predictions.txt’ ‘Example_RRDist.txt’
  ‘Example_RRDistCol.TIF’ ‘Example_RRDistGrey.TIF’ ‘GeneticA.txt’
  ‘GeneticB.txt’ ‘Inds.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘pkgload’ ‘processx’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘textshaping’
  All declared Imports should be used.
Note: found 20 marked UTF-8 strings
Note: found 2 marked Latin-1 strings
  Note: found 50022 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Undeclared package ‘monomvn’ in Rd xrefs
Namespace in Imports field not imported from: ‘Deriv’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   3.7Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘psych’ in Rd xrefs
Undeclared packages ‘tibble’, ‘htmltools’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘Rcplex’
Undeclared package ‘graph’ in Rd xrefs
'library' or 'require' call to ‘lars’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘lars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
relaxo: no visible global function definition for ‘lars’
Undefined global functions or variables:
  lars
Rd file 'cvrelaxo.Rd':
  \usage lines wider than 90 characters:
     cvrelaxo(X, Y, K = 5, phi = seq(0, 1, length = 10), max.steps = min( 2* length(Y), 2 * ncol(X)), fast = TRUE, keep.data = TRUE, warn=TR ... [TRUNCATED]

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

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

These lines will be truncated in the PDF manual.
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
duane: no visible global function definition for ‘optim’
duane.plot: no visible global function definition for ‘lines’
duane.plot: no visible global function definition for ‘legend’
duane.plot: no visible global function definition for ‘title’
littlewood.verall: no visible global function definition for ‘optim’
littlewood.verall.plot: no visible global function definition for
  ‘lines’
littlewood.verall.plot: no visible global function definition for
  ‘legend’
littlewood.verall.plot: no visible global function definition for
  ‘title’
moranda.geometric: no visible global function definition for ‘optimize’
moranda.geometric.plot: no visible global function definition for
  ‘lines’
moranda.geometric.plot: no visible global function definition for
  ‘legend’
moranda.geometric.plot: no visible global function definition for
  ‘title’
musa.okumoto: no visible global function definition for ‘optimize’
musa.okumoto.plot: no visible global function definition for ‘lines’
musa.okumoto.plot: no visible global function definition for ‘legend’
musa.okumoto.plot: no visible global function definition for ‘title’
rel.plot: no visible global function definition for ‘lines’
rel.plot: no visible global function definition for ‘segments’
rel.plot: no visible global function definition for ‘legend’
rel.plot: no visible global function definition for ‘title’
total.plot: no visible global function definition for ‘lines’
total.plot: no visible global function definition for ‘legend’
total.plot: no visible global function definition for ‘title’
Undefined global functions or variables:
  legend lines optim optimize segments title
Consider adding
  importFrom("graphics", "legend", "lines", "segments", "title")
  importFrom("stats", "optim", "optimize")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
Namespace in Imports field not imported from: ‘gWidgets2tcltk’
  All declared Imports should be used.
CapDistSlope: no visible global function definition for ‘coef’
CapDistSlope: no visible global function definition for ‘lm’
EnergyEntropyDecomp: no visible global function definition for ‘legend’
FernholzDecomp: no visible global function definition for ‘legend’
Invest: no visible global function definition for ‘par’
Invest: no visible global function definition for ‘legend’
SimMarketModel: no visible global function definition for ‘rnorm’
plot.capdist: no visible global function definition for ‘abline’
plot.capdist: no visible global function definition for ‘lm’
plot.toymkt: no visible global function definition for ‘par’
plot.toymkt: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline coef legend lm par rnorm
Consider adding
  importFrom("graphics", "abline", "legend", "par")
  importFrom("stats", "coef", "lm", "rnorm")
to your NAMESPACE file.
Undeclared package ‘magrittr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
Package suggested but not available for checking: ‘pbdRPC’
Undeclared package ‘pls’ in Rd xrefs
RearrangeData: no visible global function definition for ‘rainbow’
RearrangeData: no visible global function definition for ‘hclust’
RearrangeData: no visible global function definition for
  ‘as.dendrogram’
RearrangeData: no visible global function definition for ‘heatmap’
RearrangeData: no visible global function definition for ‘pdf’
RearrangeData: no visible global function definition for
  ‘colorRampPalette’
RearrangeData: no visible global function definition for ‘legend’
RearrangeData: no visible global function definition for ‘dev.off’
RearrangeJoseph: no visible global function definition for
  ‘write.table’
RearrangeJoseph: no visible global function definition for
  ‘as.dendrogram’
RearrangeJoseph: no visible global function definition for
  ‘order.dendrogram’
colorDendClass : colLab: no visible global function definition for
  ‘is.leaf’
colorDendClass: no visible global function definition for ‘dendrapply’
testData1: no visible global function definition for ‘runif’
testData1: no visible global function definition for ‘image’
testData2: no visible global function definition for ‘runif’
testData2: no visible global function definition for ‘image’
Undefined global functions or variables:
  as.dendrogram colorRampPalette dendrapply dev.off hclust heatmap
  image is.leaf legend order.dendrogram pdf rainbow runif write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf",
             "rainbow")
  importFrom("graphics", "image", "legend")
  importFrom("stats", "as.dendrogram", "dendrapply", "hclust", "heatmap",
             "is.leaf", "order.dendrogram", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
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.
Found the following files/directories:
  ‘A.txt’ ‘minI.txt’ ‘minJ.txt’
Note: found 6034 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘MASS’ ‘nlme’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GlobTestMissing: no visible global function definition for ‘lme’
GlobTestMissing: no visible global function definition for ‘anova’
TestStatSP: no visible global function definition for ‘pf’
TestStatSimple: no visible global function definition for ‘ginv’
TestStatSimple: no visible global function definition for ‘pf’
Undefined global functions or variables:
  anova ginv lme pf
Consider adding
  importFrom("stats", "anova", "pf")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘PackageCites.bib’
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
MBoxtest: no visible global function definition for ‘var’
jrparams: no visible global function definition for ‘prcomp’
jrparams: no visible global function definition for ‘predict’
jrparams: no visible global function definition for ‘qchisq’
jrparams: no visible global function definition for ‘qf’
Undefined global functions or variables:
  prcomp predict qchisq qf var
Consider adding
  importFrom("stats", "prcomp", "predict", "qchisq", "qf", "var")
to your NAMESPACE file.
Rd file 'jrparams.Rd':
  \usage lines wider than 90 characters:
     jrparams(BLOCK.1, BLOCK.2, ncomp = min(c(dim(BLOCK.1), dim(BLOCK.2))), Cscrit=0.6, Rscrit=0.6)

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘ggplot2’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Note: found 25 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
call.eqs: no visible global function definition for ‘write.table’
read.eqs: no visible global function definition for ‘read.fwf’
Undefined global functions or variables:
  read.fwf write.table
Consider adding
  importFrom("utils", "read.fwf", "write.table")
to your NAMESPACE file.
Rd file 'call.eqs.rd':
  \examples lines wider than 100 characters:
     ##res <- call.eqs(EQSpgm = "C:/Program Files/EQS61/WINEQS.EXE", EQSmodel = "c:/eqs61/examples/manul7.eqs", serial = "1234")

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

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘4.2’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘P.csv’ ‘correct_alpha.csv’ ‘correct_beta.csv’ ‘correct_gamma.csv’
  ‘correct_lambda.csv’ ‘correct_perm_list.csv’ ‘correct_psi.csv’
.resampleMakeFunction: no visible global function definition for ‘is’
.resampleSetSeed: no visible global function definition for ‘runif’
CI.bca: no visible global function definition for ‘is’
CI.bca: no visible global function definition for ‘qnorm’
CI.bca: no visible global function definition for ‘pnorm’
CI.t: no visible global function definition for ‘qt’
ExpandProbs: no visible global function definition for ‘pnorm’
ExpandProbs: no visible global function definition for ‘qt’
colVars : f: no visible global function definition for ‘var’
colVars: no visible global function definition for ‘var’
hist.resample: no visible global function definition for ‘density’
hist.resample: no visible global function definition for ‘lines’
hist.resample: no visible global function definition for ‘points’
hist.resample: no visible global function definition for ‘approx’
hist.resample: no visible global function definition for ‘segments’
resample: no visible global function definition for ‘is’
samp.bootknife: no visible global function definition for ‘runif’
samp.bootstrap: no visible global function definition for ‘runif’
Undefined global functions or variables:
  approx density is lines pnorm points qnorm qt runif segments var
Consider adding
  importFrom("graphics", "lines", "points", "segments")
  importFrom("methods", "is")
  importFrom("stats", "approx", "density", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GUI_template : onHelp: no visible global function definition for ‘help’
Undefined global functions or variables:
  help
Consider adding
  importFrom("utils", "help")
to your NAMESPACE file.
File ‘restrictedMVN/libs/restrictedMVN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    libs      3.2Mb
    swagger   1.4Mb
Namespace in Imports field not imported from: ‘Rserve’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    libs     15.5Mb
    models    1.6Mb
Package suggested but not available for checking: ‘gWidgets2RGtk2’

Suggests orphaned packages:
  ‘RGtk2’ ‘cairoDevice’
Namespace in Imports field not imported from: ‘RTriangle’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘phangorn’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘pkgload’
  All declared Imports should be used.
Note: found 26 marked UTF-8 strings
Undeclared package ‘robustbase’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
plot.reweight: no visible global function definition for ‘par’
plot.reweight: no visible global function definition for ‘density’
plot.reweight: no visible global function definition for ‘rug’
reweight: no visible global function definition for ‘aggregate’
search.best.h: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  aggregate density par quantile rug
Consider adding
  importFrom("graphics", "par", "rug")
  importFrom("stats", "aggregate", "density", "quantile")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Undeclared package ‘btergm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pkgload’
  All declared Imports should be used.
installed size is 23.7Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
installed size is 50.3Mb
  sub-directories of 1Mb or more:
    libs  48.9Mb
Namespace in Imports field not imported from: ‘iCluster’
  All declared Imports should be used.
FDSNGetTimeSeries: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
fs_author_ids : <anonymous>: no visible global function definition for
  ‘select.list’
fs_download : <anonymous>: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file select.list
Consider adding
  importFrom("utils", "download.file", "select.list")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘httr’ ‘lubridate’ ‘stringr’
  All declared Imports should be used.
Note: found 44 marked UTF-8 strings
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
installed size is 37.1Mb
  sub-directories of 1Mb or more:
    java  37.0Mb
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    java   5.3Mb
.testLTS: no visible binding for global variable ‘stackloss’
Undefined global functions or variables:
  stackloss
Consider adding
  importFrom("datasets", "stackloss")
to your NAMESPACE file.
Found the following files/directories:
  ‘interactions.dot’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘prob’ ‘titanic’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
gabriel.plot: no visible global function definition for ‘barplot’
gabriel.plot: no visible global function definition for ‘arrows’
rgabriel: no visible binding for global variable ‘sd’
rgabriel : psmm_x: no visible global function definition for ‘pnorm’
rgabriel : psmm: no visible global function definition for ‘integrate’
rgabriel : qsmm: no visible global function definition for ‘qnorm’
rgabriel : qsmm: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  arrows barplot integrate pnorm qnorm sd uniroot
Consider adding
  importFrom("graphics", "arrows", "barplot")
  importFrom("stats", "integrate", "pnorm", "qnorm", "sd", "uniroot")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Package in Depends field not imported from: ‘gsl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gammaIntegral: no visible global function definition for ‘integrate’
gammaIntegral : <anonymous>: no visible global function definition for
  ‘hyperg_1F1’
gammaMLE: no visible global function definition for ‘weighted.mean’
gammaMME: no visible binding for global variable ‘sd’
gammaMME: no visible binding for global variable ‘var’
Undefined global functions or variables:
  hyperg_1F1 integrate sd var weighted.mean
Consider adding
  importFrom("stats", "integrate", "sd", "var", "weighted.mean")
to your NAMESPACE file.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       2.2Mb
    extdata   2.7Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc        3.4Mb
    pictures   1.3Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
genoud: multiple local function definitions for ‘fn1.bfgs’ with
  different formal arguments
genoud: multiple local function definitions for ‘gr1’ with different
  formal arguments
genoud: multiple local function definitions for ‘hess.fn’ with
  different formal arguments
genoud_transform: multiple local function definitions for ‘fn1.bfgs’
  with different formal arguments
genoud_transform: multiple local function definitions for ‘gr1’ with
  different formal arguments
Undeclared package ‘Matching’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    libs  25.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
    libs      1.6Mb
Namespaces in Imports field not imported from:
  ‘leaflet’ ‘pals’ ‘raster’ ‘sp’
  All declared Imports should be used.
Running examples in ‘rgexf-Ex.R’ failed
The error most likely occurred in:

> ### Name: igraph.to.gexf
> ### Title: Converting between 'gexf' and 'igraph' classes
> ### Aliases: igraph.to.gexf gexf.to.igraph
> ### Keywords: manip
> 
> ### ** Examples
> 
> 
> if (interactive()) {
+   # Running demo
+   demo(gexfigraph)
+ }
>  
>   fn <- system.file("gexf-graphs/lesmiserables.gexf", package = "rgexf")
>   gexf1 <- read.gexf(fn)
>   igraph1 <- gexf.to.igraph(gexf1)
>   gexf2 <- igraph.to.gexf(igraph1)
Error in parseVizAtt(a, b, n, "nodes") : 
  The attribute -position- has incorrect length (has 3, and must have 77).
Calls: igraph.to.gexf ... <Anonymous> -> Map -> mapply -> <Anonymous> -> parseVizAtt
Execution halted
Running ‘tinytest.R’
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   tinytest::test_package("rgexf")
  + }
  
  test-bugs.r...................    0 tests    
  test-bugs.r...................    0 tests    
  test-bugs.r...................    1 tests [0;32mOK[0m 
  test-bugs.r...................    1 tests [0;32mOK[0m 
  test-bugs.r...................    1 tests [0;32mOK[0m 
  test-bugs.r...................    2 tests [0;32mOK[0m [0;34m0.2s[0m
  [0;36m2ms[0m
  
  test-igraph.r.................    0 tests    
  test-igraph.r.................    0 tests    
  test-igraph.r.................    0 tests    
  test-igraph.r.................    0 tests    
  test-igraph.r.................    0 tests    
  test-igraph.r.................    0 tests    Error in parseVizAtt(a, b, n, "nodes") : 
    The attribute -position- has incorrect length (has 3, and must have 10).
  Calls: <Anonymous> ... <Anonymous> -> Map -> mapply -> <Anonymous> -> parseVizAtt
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘rgexf.Rmd’ using rmarkdown
Quitting from lines 63-64 (rgexf.Rmd) 
Error: processing vignette 'rgexf.Rmd' failed with diagnostics:
The attribute -position- has incorrect length (has 3, and must have 77).
--- failed re-building ‘rgexf.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Undeclared packages ‘lpSolve’, ‘ROI’, ‘Rsymphony’ in Rd xrefs
Package suggested but not available for checking: ‘webshot2’
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    fonts     1.5Mb
    libs      2.7Mb
    useNULL   1.9Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘cachem’ ‘magrittr’ ‘rappdirs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MD_display.csv’ ‘kola.c_COUNTRY_Cu.csv’
  ‘kola.c_COUNTRY_Cu_fences.txt’ ‘ogrady.mvalloc_mvalloc.csv’
  ‘sind.mat2open_NGR_summary.csv’ ‘sind.save_PC-loadings.csv’
  ‘sind.save_PC-scores.csv’ ‘test.save.mvalloc_mvalloc.csv’
'LazyData' is specified without a 'data' directory
installed size is 25.7Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.6Mb
    libs   9.7Mb
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.
Note: found 1473 marked UTF-8 strings
Undeclared package ‘DBI’ in Rd xrefs
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc          10.3Mb
    htmlwidgets   1.3Mb
.quick_fetch: no visible global function definition for ‘POST’
.quick_fetch: no visible global function definition for ‘add_headers’
.quick_fetch: no visible global function definition for
  ‘stop_for_status’
.quick_fetch: no visible global function definition for ‘content’
fetch_healthdata: no visible binding for global variable ‘resources’
fetch_healthdata : <anonymous>: no visible binding for global variable
  ‘filters’
Undefined global functions or variables:
  POST add_headers content filters resources stop_for_status
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘mydata.rda’ ‘thedata.rda’
'LazyData' is specified without a 'data' directory
Packages in Depends field not imported from:
  ‘RCurl’ ‘XML’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ECL: no visible global function definition for ‘new’
ECLDataset: no visible global function definition for ‘new’
ECLDedUp: no visible global function definition for ‘new’
ECLDistribute: no visible global function definition for ‘new’
ECLIterate: no visible global function definition for ‘new’
ECLJoin: no visible global function definition for ‘new’
ECLOutput: no visible global function definition for ‘new’
ECLProject: no visible global function definition for ‘new’
ECLRecord: no visible global function definition for ‘new’
ECLRollUp: no visible global function definition for ‘new’
ECLSort: no visible global function definition for ‘new’
ECLTOPN: no visible global function definition for ‘new’
ECLTable: no visible global function definition for ‘new’
ECLTransform: no visible global function definition for ‘new’
eclDirectCall: no visible global function definition for ‘postForm’
parseResults: no visible global function definition for ‘xmlRoot’
parseResults: no visible global function definition for ‘xmlTreeParse’
parseResults: no visible global function definition for ‘getNodeSet’
parseResults: no visible global function definition for ‘xmlGetAttr’
parseResults: no visible global function definition for ‘xmlValue’
parseResults: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  getNodeSet new postForm write.table xmlGetAttr xmlRoot xmlTreeParse
  xmlValue
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Undeclared packages ‘tseries’, ‘TSA’ in Rd xrefs
'LazyData' is specified without a 'data' directory
RHT.2samp : my.HotellingT2 : my.InvCov2: no visible global function
  definition for ‘cov’
RHT.2samp : get.lambda : get.para: no visible global function
  definition for ‘optimize’
RHT.2samp : get.lambda : gg: no visible global function definition for
  ‘qchisq’
RHT.2samp : get.lambda : ggl: no visible global function definition for
  ‘qnorm’
RHT.2samp : <anonymous>: no visible global function definition for
  ‘cov’
RHT.fun : my.HotellingT : my.InvCov: no visible global function
  definition for ‘cov’
RHT.fun : get.lambda : get.para: no visible global function definition
  for ‘optimize’
RHT.fun : get.lambda : gg: no visible global function definition for
  ‘qchisq’
RHT.fun : get.lambda : ggl: no visible global function definition for
  ‘qnorm’
RHT.fun : <anonymous>: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov optimize qchisq qnorm
Consider adding
  importFrom("stats", "cov", "optimize", "qchisq", "qnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
Namespace in Imports field not imported from: ‘glue’
  All declared Imports should be used.
FusedQDA : <anonymous>: no visible global function definition for ‘cov’
RidgeFused: no visible binding for global variable ‘cov2cor’
RidgeFusedCV : <anonymous>: no visible global function definition for
  ‘cov’
SSRidgeFused : <anonymous>: no visible global function definition for
  ‘cov’
Undefined global functions or variables:
  cov cov2cor
Consider adding
  importFrom("stats", "cov", "cov2cor")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
ridit.raw: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
Namespace in Imports field not imported from: ‘ggrepel’
  All declared Imports should be used.
Undeclared packages ‘dtw’, ‘fastcluster’, ‘Rtsne’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
R2ngon: no visible global function definition for ‘approx’
plotR2pre: no visible global function definition for ‘points’
plotR2pre: no visible global function definition for ‘gray’
plotR2pre: no visible global function definition for ‘legend’
plotR2pre: no visible global function definition for ‘rainbow’
Undefined global functions or variables:
  approx gray legend points rainbow
Consider adding
  importFrom("grDevices", "gray", "rainbow")
  importFrom("graphics", "legend", "points")
  importFrom("stats", "approx")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘Exact’ ‘plyr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rmarkdown’ ‘stringr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lifecycle’
  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’

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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
desmat.sanitize: no visible global function definition for ‘aggregate’
dispdist: no visible global function definition for ‘quantile’
dispdist: no visible global function definition for ‘hist’
dispdist: no visible global function definition for ‘lines’
estate: no visible global function definition for ‘weighted.mean’
estate: no visible global function definition for ‘lm’
genperms: no visible global function definition for ‘combn’
genprobexact: no visible global function definition for ‘ave’
invert.ci: no visible global function definition for ‘quantile’
invert.ci: no visible global function definition for ‘uniroot’
omni.ate: no visible global function definition for ‘hist’
omni.ate: no visible global function definition for ‘lines’
omni.ate: no visible global function definition for ‘quantile’
resresplot: no visible global function definition for ‘lm’
resresplot: no visible global function definition for ‘symbols’
resresplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline aggregate ave combn hist lines lm quantile symbols uniroot
  weighted.mean
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "symbols")
  importFrom("stats", "aggregate", "ave", "lm", "quantile", "uniroot",
             "weighted.mean")
  importFrom("utils", "combn")
to your NAMESPACE file.
Rd file 'genperms.custom.Rd':
  \examples lines wider than 100 characters:
                     teststat <- pf(fstat[1],fstat[2],fstat[3],lower.tail=FALSE)  # extract F-test p-value

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

These lines will be truncated in the PDF manual.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
'LazyData' is specified without a 'data' directory
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.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  21.5Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
KM.plot: no visible global function definition for ‘lines’
SchoenSmooth: no visible global function definition for ‘lm’
llCoxReg: no visible binding for global variable ‘time’
risksetAUC: no visible global function definition for ‘abline’
risksetROC: no visible global function definition for ‘abline’
weightedKM: no visible binding for global variable ‘time’
Undefined global functions or variables:
  abline lines lm time
Consider adding
  importFrom("graphics", "abline", "lines")
  importFrom("stats", "lm", "time")
to your NAMESPACE file.
Alg2: no visible global function definition for ‘uniroot’
Alg3: no visible global function definition for ‘optim’
NVCopula: no visible global function definition for ‘rnorm’
NVCopula: no visible global function definition for ‘rgamma’
NVCopula: no visible global function definition for ‘var’
NVCopula: no visible global function definition for ‘cov’
NVCopula: no visible global function definition for ‘qnorm’
NVCopulaMT: no visible global function definition for ‘rnorm’
NVCopulaMT: no visible global function definition for ‘rgamma’
NVCopulaMT: no visible global function definition for ‘var’
NVCopulaMT: no visible global function definition for ‘cov’
NVCopulaMT: no visible global function definition for ‘qnorm’
R2X: no visible global function definition for ‘write.table’
ReturnCopula: no visible global function definition for ‘qt’
ReturnCopula: no visible global function definition for ‘pt’
SISCopula: no visible global function definition for ‘runif’
SISCopula: no visible global function definition for ‘qnorm’
SISCopula: no visible global function definition for ‘rnorm’
SISCopula: no visible global function definition for ‘qgamma’
SISCopula: no visible global function definition for ‘var’
SISCopula: no visible global function definition for ‘cov’
SISCopulaMT: no visible global function definition for ‘runif’
SISCopulaMT: no visible global function definition for ‘qnorm’
SISCopulaMT: no visible global function definition for ‘rnorm’
SISCopulaMT: no visible global function definition for ‘qgamma’
SISCopulaMT: no visible global function definition for ‘var’
SISCopulaMT: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov optim pt qgamma qnorm qt rgamma rnorm runif uniroot var
  write.table
Consider adding
  importFrom("stats", "cov", "optim", "pt", "qgamma", "qnorm", "qt",
             "rgamma", "rnorm", "runif", "uniroot", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Note: found 243 marked UTF-8 strings
Found the following files/directories:
  ‘B110711CD4.CSV’ ‘inputparam2.txt’ ‘itcout0.pdf’ ‘itcout1.eps’
  ‘origin_data.csv’
Package suggested but not available for checking: ‘RSVGTipsDevice’
'LazyData' is specified without a 'data' directory
Undeclared package ‘utility’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Packages in Depends field not imported from:
  ‘compiler’ ‘signal’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NumConv: no visible global function definition for ‘pchip’
NumConv: no visible global function definition for ‘cmpfun’
NumDeconv: no visible global function definition for ‘pchip’
NumDeconv : error_function: no visible global function definition for
  ‘pchip’
NumDeconv: no visible global function definition for ‘cmpfun’
NumDeconv: no visible global function definition for ‘optim’
RivivcA: no visible global function definition for ‘lm’
Undefined global functions or variables:
  cmpfun lm optim pchip
Consider adding
  importFrom("stats", "lm", "optim")
to your NAMESPACE file.
Rd file 'NumConv.Rd':
  \usage lines wider than 90 characters:
     NumConv(impulse.matrix, input.matrix, conv.timescale = NULL, explicit.interpolation = 1000)

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

These lines will be truncated in the PDF manual.
Found the following possibly unsafe calls:
File ‘rJava/R/import.R’:
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File ‘rJava/R/jinit.R’:
  unlockBinding(x, .env)
  unlockBinding(x, pe)
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files is not available
File ‘/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’

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.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/RJDemetra.Rcheck/00install.out’ for details.
Package required but not available: ‘RJDemetra’

Package suggested but not available for checking: ‘ggdemetra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RJDemetra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘coda’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
File
  LICENSE
is not mentioned in the DESCRIPTION file.
'library' or 'require' call to ‘rJava’ which was already attached by Depends.
  Please remove these calls from your code.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  21.0Mb
cv.coef: no visible global function definition for ‘sd’
normalize.softmax: no visible global function definition for ‘plogis’
plot.rknnSupport: no visible global function definition for ‘dotchart’
predicted: no visible global function definition for ‘influence’
predicted: no visible global function definition for ‘fitted’
predicted: no visible global function definition for ‘resid’
pressresid: no visible global function definition for ‘influence’
pressresid: no visible global function definition for ‘resid’
Undefined global functions or variables:
  dotchart fitted influence plogis resid sd
Consider adding
  importFrom("graphics", "dotchart")
  importFrom("stats", "fitted", "influence", "plogis", "resid", "sd")
to your NAMESPACE file.
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    extdata  24.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
Malformed Description field: should contain one or more complete sentences.
':::' calls which should be '::':
  ‘stats:::dexp’ ‘stats:::dgamma’ ‘stats:::dweibull’ ‘stats:::pexp’
  ‘stats:::pgamma’ ‘stats:::pweibull’ ‘stats:::qexp’ ‘stats:::qgamma’
  ‘stats:::qweibull’ ‘stats:::rexp’ ‘stats:::rgamma’ ‘stats:::rweibull’
  See the note in ?`:::` about the use of this operator.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Undeclared package ‘rgdal’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is 49.7Mb
  sub-directories of 1Mb or more:
    libs  49.1Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RCarb’ ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
Found the following files/directories:
  ‘file.out’
Package in Depends field not imported from: ‘msm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘EMSRb_internal’ ‘EM_internal’ ‘PD_internal’
EMSRb_internal: no visible global function definition for ‘qnorm’
EM_internal: no visible global function definition for ‘dnorm’
EM_internal: no visible global function definition for ‘pnorm’
PD_internal: no visible global function definition for ‘qtnorm’
PD_internal: no visible global function definition for ‘sd’
Undefined global functions or variables:
  dnorm pnorm qnorm qtnorm sd
Consider adding
  importFrom("stats", "dnorm", "pnorm", "qnorm", "sd")
to your NAMESPACE file.
Rd file 'EMSRb_internal.Rd':
  \usage lines wider than 90 characters:
     EMSRb_internal(Fare = Fare, Mean = Mean, Var = Var, p_up = numeric(length(Fare)), cap = cap)

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

> ### Name: RMaCzek
> ### Title: RMaCzek: A package that can produce Czekanowski's diagram
> ### Aliases: RMaCzek RMaCzek-package
> ### Keywords: hplot
> 
> ### ** Examples
> 
> # Set data ####
> x<-czek_matrix(mtcars)
Error in ser_permutation_vector(order, method = method$name) : 
  'list' object cannot be coerced to type 'integer'
Calls: czek_matrix ... seriate.dist -> ser_permutation -> ser_permutation_vector
Execution halted
'LazyData' is specified without a 'data' directory
ma.filter: no visible global function definition for ‘par’
ma.filter: no visible global function definition for ‘lines’
ma.filter: no visible global function definition for ‘abline’
qn: no visible global function definition for ‘lm’
qn: no visible global function definition for ‘var’
qn: no visible global function definition for ‘resid’
ss.filter: no visible global function definition for ‘smooth.spline’
ss.filter: no visible global function definition for ‘par’
ss.filter: no visible global function definition for ‘lines’
ss.filter: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline lines lm par resid smooth.spline var
Consider adding
  importFrom("graphics", "abline", "lines", "par")
  importFrom("stats", "lm", "resid", "smooth.spline", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Note: found 31 marked UTF-8 strings
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    rmd   8.2Mb
Found the following files/directories:
  ‘dipper.inp’ ‘mark001.inp’ ‘mark001.out’ ‘mark001.res’ ‘mark001.vcv’
  ‘mark002.inp’ ‘mark002.out’ ‘mark002.res’ ‘mark002.vcv’ ‘mark003.inp’
  ‘mark003.out’ ‘mark003.res’ ‘mark003.vcv’ ‘mark004.inp’ ‘mark004.out’
  ‘mark004.res’ ‘mark004.vcv’ ‘mark005.inp’ ‘mark005.out’ ‘mark005.res’
  ‘mark005.vcv’ ‘mark006.inp’ ‘mark006.out’ ‘mark006.res’ ‘mark006.vcv’
  ‘mark007.inp’ ‘mark007.out’ ‘mark007.res’ ‘mark007.vcv’ ‘mark008.inp’
  ‘mark008.out’ ‘mark008.res’ ‘mark008.vcv’ ‘mark009.inp’ ‘mark009.out’
  ‘mark009.res’ ‘mark009.vcv’ ‘mark010.inp’ ‘mark010.out’ ‘mark010.res’
  ‘mark010.vcv’ ‘mark010V.tmp’ ‘mark010X.tmp’ ‘mark010Y.tmp’
  ‘mark011.inp’ ‘mark011.out’ ‘mark011.res’ ‘mark011.vcv’ ‘mark012.inp’
  ‘mark012.out’ ‘mark012.res’ ‘mark012.vcv’ ‘mark013.inp’ ‘mark013.out’
  ‘mark013.res’ ‘mark013.vcv’
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
installed size is 133.6Mb
  sub-directories of 1Mb or more:
    libs  133.2Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 60.9Mb
  sub-directories of 1Mb or more:
    libs  60.1Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘R.oo’ in Rd xrefs
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs       1.1Mb
    minizinc   3.4Mb
'LazyData' is specified without a 'data' directory
CI: no visible global function definition for ‘sd’
CI: no visible global function definition for ‘qt’
L: no visible global function definition for ‘sd’
L: no visible global function definition for ‘residuals’
Qa: no visible global function definition for ‘logLik’
Qb: no visible global function definition for ‘residuals’
Qc: no visible global function definition for ‘residuals’
Qc: no visible global function definition for ‘logLik’
STDERR: no visible global function definition for ‘sd’
group.UCL: no visible global function definition for ‘aggregate’
lr.glover: no visible binding for global variable ‘logLik’
lr.glover: no visible binding for global variable ‘update’
lr.glover : nobs0: no visible binding for global variable ‘nobs’
lr.glover : nobs0 : nobs2: no visible global function definition for
  ‘residuals’
lr.glover : tlab: no visible global function definition for ‘terms’
lr.glover : name: no visible global function definition for ‘formula’
lr.glover : modelUpdate: no visible global function definition for
  ‘as.formula’
lr.glover: no visible global function definition for ‘model.frame’
lr.glover: no visible binding for global variable ‘AIC’
lr.glover: no visible binding for global variable ‘BIC’
summarySE : <anonymous>: no visible global function definition for ‘sd’
summarySE: no visible global function definition for ‘qt’
Undefined global functions or variables:
  AIC BIC aggregate as.formula formula logLik model.frame nobs qt
  residuals sd terms update
Consider adding
  importFrom("stats", "AIC", "BIC", "aggregate", "as.formula", "formula",
             "logLik", "model.frame", "nobs", "qt", "residuals", "sd",
             "terms", "update")
to your NAMESPACE file.
Combi: no visible global function definition for ‘new’
barplotMixCluster: no visible global function definition for ‘is’
barplotMixCluster: no visible global function definition for ‘par’
barplotMixCluster: no visible global function definition for ‘lines’
barplotMixCluster: no visible global function definition for ‘text’
barplotMixCluster: no visible global function definition for ‘title’
barplotMixCluster: no visible global function definition for ‘mtext’
histMixCluster: no visible global function definition for ‘is’
histMixCluster: no visible global function definition for ‘par’
histMixCluster: no visible global function definition for ‘dnorm’
histMixCluster: no visible global function definition for ‘lines’
mixmodEntPlot: no visible global function definition for ‘par’
mixmodEntPlot: no visible global function definition for ‘lines’
mixmodEntPlot: no visible global function definition for ‘axis’
mixmodEntPlot: no visible global function definition for ‘title’
mixmodEntPlot: no visible binding for global variable ‘par’
plot,MixmodCombi: no visible global function definition for ‘par’
plot,MixmodCombi: no visible global function definition for ‘plot.new’
plot,MixmodCombi: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis dnorm is lines mtext new par plot.new text title
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par", "plot.new",
             "text", "title")
  importFrom("methods", "is", "new")
  importFrom("stats", "dnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘RmixmodCombi-Ex.R’ failed
The error most likely occurred in:

> ### Name: Baudry_etal_2010_JCGS_examples
> ### Title: Simulated Example Datasets From Baudry et al. (2010)
> ### Aliases: Baudry_etal_2010_JCGS_examples Test1D ex4.1 ex4.2 ex4.3
> ###   ex4.4.1 ex4.4.2
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> set.seed(1)
> 
> data(Baudry_etal_2010_JCGS_examples)
> 
> output <- mixmodCombi(ex4.4.2, nbCluster = 1:10, 
+ models = mixmodGaussianModel(listModels = "Gaussian_pk_Lk_Ck")) 
Warning in xtfrm.data.frame(x) : cannot xtfrm data frames
Warning in is.dataType(data) :
  more than 25% of the observations have different modalities
Warning in xtfrm.data.frame(x) : cannot xtfrm data frames
Warning in isQualitative(x) :
  more than 25% of the observations have different modalities
Warning in xtfrm.data.frame(x) : cannot xtfrm data frames
Error in validityMethod(as(object, superClass)) : 
  number of factors too small!
Calls: mixmodCombi ... validObject -> anyStrings -> isTRUE -> validityMethod
Execution halted
installed size is 34.6Mb
  sub-directories of 1Mb or more:
    libs  33.7Mb
Running examples in ‘Rmixmod-Ex.R’ failed
The error most likely occurred in:

> ### Name: MixmodCluster-class
> ### Title: Constructor of ['MixmodCluster'] class
> ### Aliases: MixmodCluster-class
> 
> ### ** Examples
> 
>   ## A quantitative example with the famous iris data set
>   data(iris)
>   ## with default values
>   new("MixmodCluster", data=iris[1:4], nbCluster=3)
Warning in xtfrm.data.frame(x) : cannot xtfrm data frames
Warning in is.dataType(data) :
  more than 25% of the observations have different modalities
Warning in xtfrm.data.frame(x) : cannot xtfrm data frames
Warning in isQualitative(x) :
  more than 25% of the observations have different modalities
Warning in xtfrm.data.frame(x) : cannot xtfrm data frames
Error in validityMethod(as(object, superClass)) : 
  number of factors too small!
Calls: new ... validObject -> anyStrings -> isTRUE -> validityMethod
Execution halted
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    libs  26.9Mb
.pLGP_qvec: no visible global function definition for ‘ppois’
.qLGP_pvec: no visible global function definition for ‘qpois’
.rLGP.failsafe: no visible global function definition for ‘runif’
.subdmg: no visible global function definition for ‘dbinom’
dnegbin: no visible global function definition for ‘dnbinom’
pLGP: no visible global function definition for ‘ppois’
qLGP: no visible global function definition for ‘qpois’
rLGP: no visible global function definition for ‘rpois’
rLGP: no visible global function definition for ‘rnorm’
rLGP: no visible global function definition for ‘runif’
rbinegbin: no visible global function definition for ‘rnbinom’
rmanaclash: no visible global function definition for ‘rbinom’
rmanaclash: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbinom dnbinom ppois qpois rbinom rnbinom rnorm rpois runif
Consider adding
  importFrom("stats", "dbinom", "dnbinom", "ppois", "qpois", "rbinom",
             "rnbinom", "rnorm", "rpois", "runif")
to your NAMESPACE file.
File ‘RMKdiscrete/libs/RMKdiscrete.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is 47.9Mb
  sub-directories of 1Mb or more:
    libs  47.3Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
Undeclared package ‘coda’ in Rd xrefs
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Undeclared package ‘fortunes’ in Rd xrefs
'LazyData' is specified without a 'data' directory
rms.pval: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
dWishartSpike: no visible global function definition for ‘dnorm’
pWishartSpike: no visible global function definition for ‘pnorm’
qWishartSpike: no visible global function definition for ‘qnorm’
rWishartSpike: no visible global function definition for ‘qnorm’
rmp: no visible global function definition for ‘runif’
rtw: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dnorm pnorm qnorm runif
Consider adding
  importFrom("stats", "dnorm", "pnorm", "qnorm", "runif")
to your NAMESPACE file.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
File ‘RMVL/libs/RMVL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is 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  17.0Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 133 marked Latin-1 strings
Package suggested but not available for checking: ‘rnaturalearthhires’
Note: found 7 marked Latin-1 strings
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Undeclared packages ‘fossil’, ‘raster’ in Rd xrefs
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘qtl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘rngSetSeed/libs/rngSetSeed.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is 88.7Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     86.6Mb
'LazyData' is specified without a 'data' directory
Nnls.trimW : fun1: no visible global function definition for ‘runif’
initM: no visible global function definition for ‘runif’
rnmf: no visible global function definition for ‘txtProgressBar’
rnmf: no visible global function definition for ‘setTxtProgressBar’
see: no visible global function definition for ‘heat.colors’
see: no visible global function definition for ‘colorRampPalette’
see: no visible global function definition for ‘grey’
see: no visible global function definition for ‘par’
see: no visible global function definition for ‘image’
see: no visible global function definition for ‘mtext’
simtum: no visible global function definition for ‘runif’
simtum: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  colorRampPalette grey heat.colors image mtext par rnorm runif
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey", "heat.colors")
  importFrom("graphics", "image", "mtext", "par")
  importFrom("stats", "rnorm", "runif")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘impute’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘rappdirs’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.7Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R  11.2Mb
'LazyData' is specified without a 'data' directory
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  15.0Mb
Undeclared package ‘StatDA’ in Rd xrefs
Note: found 1 marked UTF-8 string
Running examples in ‘robCompositions-Ex.R’ failed
The error most likely occurred in:

> ### Name: aDist
> ### Title: Aitchison distance
> ### Aliases: aDist iprod
> ### Keywords: arith math
> 
> ### ** Examples
> 
> 
> data(expenditures)
> x <- xOrig <- expenditures
> ## Aitchison distance between two 2 observations:
> aDist(x[1, ], x[2, ])
[1] 1.626736
> 
> ## Aitchison distance of x:
> aDist(x)
Error in na.omit(x == 0) : 
  'list' object cannot be coerced to type 'double'
Calls: aDist ... dist -> as.matrix -> cenLR -> apply -> FUN -> na.omit
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘imputation.Rnw’ using knitr
Quitting from lines 569-571 (imputation.Rnw) 
Error: processing vignette 'imputation.Rnw' failed with diagnostics:
x must be a matrix or data frame
--- failed re-building ‘imputation.Rnw’

--- re-building ‘robCompositions-overview.Rnw’ using Sweave
--- finished re-building ‘robCompositions-overview.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'library' or 'require' calls in package code:
  ‘robustbase’ ‘sfsmisc’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.BuildPartial: no visible global function definition for ‘as.formula’
.BuildPartial: no visible global function definition for ‘residuals’
.PairwiseCorrelation : .Standardize : <anonymous>: no visible global
  function definition for ‘na.omit’
.PairwiseCorrelation : .Standardize: no visible binding for global
  variable ‘median’
.PairwiseCorrelation: no visible global function definition for
  ‘complete.cases’
.yw: no visible global function definition for ‘toeplitz’
FastQn: no visible global function definition for ‘median’
FastQn: no visible global function definition for ‘mad’
fqn: no visible global function definition for ‘median’
fqn: no visible global function definition for ‘mad’
psdcor: no visible global function definition for ‘posdefify’
psdcor: no visible global function definition for ‘nearcor’
robar: no visible global function definition for ‘frequency’
robcor: no visible global function definition for ‘covMcd’
s_FastQn: no visible global function definition for ‘median’
Undefined global functions or variables:
  as.formula complete.cases covMcd frequency mad median na.omit nearcor
  posdefify residuals toeplitz
Consider adding
  importFrom("stats", "as.formula", "complete.cases", "frequency", "mad",
             "median", "na.omit", "residuals", "toeplitz")
to your NAMESPACE file.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Undeclared package ‘ggm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  22.7Mb
Undeclared package ‘distrEx’ in Rd xrefs
Undeclared package ‘ROptEst’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘bridgesampling’ ‘callr’ ‘extraDistr’ ‘psych’ ‘runjags’
  All declared Imports should be used.
Undeclared package ‘metafor’ in Rd xrefs
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
RobRSVD: no visible global function definition for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
Undeclared package ‘svdvisual’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘graphics’ ‘methods’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 6 marked UTF-8 strings
Running examples in ‘robustbase-Ex.R’ failed
The error most likely occurred in:

> ### Name: Animals2
> ### Title: Brain and Body Weights for 65 Species of Land Animals
> ### Aliases: Animals2
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Animals2)
> ## Sensible Plot needs doubly logarithmic scale
> plot(Animals2, log = "xy")
> 
> ## Regression example plot:
> plotbb <- function(bbdat) {
+   d.name <- deparse(substitute(bbdat))
+   plot(log(brain) ~ log(body), data = bbdat, main = d.name)
+   abline(       lm(log(brain) ~ log(body), data = bbdat))
+   abline(MASS::rlm(log(brain) ~ log(body), data = bbdat), col = 2)
+   legend("bottomright", leg = c("lm", "rlm"), col=1:2, lwd=1, inset = 1/20)
+ }
> plotbb(bbdat = Animals2)
> 
> ## The `same' plot for Rousseeuw's subset:
> data(Animals, package = "MASS")
> brain <- Animals[c(1:24, 26:25, 27:28),]
> plotbb(bbdat = brain)
> 
> lbrain <- log(brain)
> plot(mahalanobis(lbrain, colMeans(lbrain), var(lbrain)),
+      main = "Classical Mahalanobis Distances")
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'plot': non-numeric argument to binary operator
Calls: plot -> mahalanobis -> sweep -> .handleSimpleError -> h
Execution halted
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
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.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘RcppArmadillo’ ‘mgcv’ ‘robustbase’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GIC: no visible global function definition for ‘integrate’
QM.poisson: no visible global function definition for ‘ppois’
QM.poisson: no visible global function definition for ‘dpois’
expect.poisson: no visible global function definition for ‘dpois’
expect.poisson: no visible global function definition for ‘ppois’
pred.robustgam: no visible global function definition for
  ‘Predict.matrix’
robust.sigma: no visible global function definition for ‘median’
robustgam: no visible global function definition for ‘s’
robustgam: no visible global function definition for
  ‘smooth.construct.tp.smooth.spec’
robustgam: no visible global function definition for
  ‘smooth.construct.cr.smooth.spec’
robustgam: no visible global function definition for
  ‘smooth.construct.ps.smooth.spec’
robustgam : w.fun: no visible global function definition for ‘covMcd’
robustgam.GIC.optim: no visible global function definition for ‘optim’
robustgam.crossval : w.fun: no visible global function definition for
  ‘covMcd’
robustgam.crossval: no visible global function definition for
  ‘integrate’
smooth.construct.tr.smooth.spec: no visible global function definition
  for ‘quantile’
w.binomial: no visible global function definition for ‘pbinom’
w.poisson: no visible global function definition for ‘ppois’
Undefined global functions or variables:
  Predict.matrix covMcd dpois integrate median optim pbinom ppois
  quantile s smooth.construct.cr.smooth.spec
  smooth.construct.ps.smooth.spec smooth.construct.tp.smooth.spec
Consider adding
  importFrom("stats", "dpois", "integrate", "median", "optim", "pbinom",
             "ppois", "quantile")
to your NAMESPACE file.
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 25.8Mb
  sub-directories of 1Mb or more:
    libs  25.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    libs  28.0Mb
'LazyData' is specified without a 'data' directory
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.
aggregateRanks: no visible binding for global variable ‘median’
aggregateRanks: no visible global function definition for ‘pnorm’
betaScores: no visible global function definition for ‘pbeta’
correctBetaPvaluesExact: no visible binding for global variable ‘qbeta’
thresholdBetaScore: no visible global function definition for ‘pbeta’
Undefined global functions or variables:
  median pbeta pnorm qbeta
Consider adding
  importFrom("stats", "median", "pbeta", "pnorm", "qbeta")
to your NAMESPACE file.
Undeclared package ‘pcaPP’ in Rd xrefs
Running examples in ‘robustX-Ex.R’ failed
The error most likely occurred in:

> ### Name: mvBACON
> ### Title: BACON: Blocked Adaptive Computationally-Efficient Outlier
> ###   Nominators
> ### Aliases: mvBACON
> ### Keywords: multivariate robust
> 
> ### ** Examples
> 
>  require(robustbase) # for example data and covMcd():
Loading required package: robustbase
>  ## simple 2D example :
>  plot(starsCYG, main = "starsCYG  data  (n=47)")
>  B.st <- mvBACON(starsCYG)
Error in FUN(x, aperm(array(STATS, dims[perm]), order(perm)), ...) : 
  non-numeric argument to binary operator
Calls: mvBACON -> order -> mahalanobis -> sweep
Execution halted
Undeclared packages ‘mvtnorm’, ‘scatterplot3d’, ‘HH’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘RODBC’
A package should be listed in only one of these fields.
'library' or 'require' call to ‘RODBC’ which was already attached by Depends.
  Please remove these calls from your code.
Package required but not available: ‘clpAPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 261 marked UTF-8 strings
Running examples in ‘rollinglda-Ex.R’ failed
The error most likely occurred in:

> ### Name: RollingLDA
> ### Title: RollingLDA
> ### Aliases: RollingLDA RollingLDA.default
> 
> ### ** Examples
> 
> roll_lda = RollingLDA(texts = economy_texts,
+                       dates = economy_dates,
+                       chunks = "quarter",
+                       memory = "3 quarter",
+                       init = "2008-07-03",
+                       K = 10,
+                       type = "lda")
Fitting LDA as initial model.
No seeds given or length of given seeds differs from number of replications: sample seeds. Sampled seeds can be obtained via getJob().
Exporting objects to package env on master for mode: local
Error in getLDA.LDARep(LDARep(docs = docs, vocab = vocab, n = 1, ...)) : 
  Assertion on 'job$job.id' failed: Element 3 is not >= 1.
Calls: RollingLDA ... getLDA.LDARep -> assert_integerish -> makeAssertion -> mstop
Execution halted
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   2.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    libs  20.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘readroper’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘pROC’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘diptest’ ‘methods’ ‘viridis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘rosm.Rmd’ using rmarkdown
Using default API key for pickpoint.io. If batch geocoding, please get your own (free) API key at https://app.pickpoint.io/sign-up
Quitting from lines 35-38 (rosm.Rmd) 
Error: processing vignette 'rosm.Rmd' failed with diagnostics:
attempt to select less than one element in get1index
--- failed re-building ‘rosm.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.7Mb
    libs   5.1Mb
bestFM: no visible global function definition for ‘data’
gaRoth: no visible global function definition for ‘data’
ros: no visible global function definition for ‘na.omit’
rosunc: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  data na.omit rnorm
Consider adding
  importFrom("stats", "na.omit", "rnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
Package suggested but not available for checking: ‘fulltext’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
.computeValueReduct: no visible global function definition for ‘combn’
.findAllReductsFromCore: no visible global function definition for
  ‘combn’
.findFirstReductsFromCore: no visible global function definition for
  ‘combn’
.findSmallestReductFamilyFromCore: no visible global function
  definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘geometry’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(Routliers)
  > 
  > test_check("Routliers")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-outliers_mahalanobis.R:12:1): (code run outside of `test_that()`) ──
  Error in `FUN(x, aperm(array(STATS, dims[perm]), order(perm)), ...)`: non-numeric argument to binary operator
  Backtrace:
      █
   1. ├─Routliers::outliers_mahalanobis(x = data.frame(SOC, HSC), na.rm = T) test-outliers_mahalanobis.R:12:0
   2. └─Routliers:::outliers_mahalanobis.default(...)
   3.   └─Routliers:::outliers_mahalanobisEst(x, alpha, na.rm)
   4.     └─stats::mahalanobis(data, colMeans(data), cov(data))
   5.       └─base::sweep(x, 2L, center)
  ── Error (test-outliers_mcd.R:12:1): (code run outside of `test_that()`) ───────
  Error in `FUN(x, aperm(array(STATS, dims[perm]), order(perm)), ...)`: non-numeric argument to binary operator
  Backtrace:
      █
   1. ├─Routliers::outliers_mcd(x = data.frame(SOC, HSC), na.rm = T) test-outliers_mcd.R:12:0
   2. └─Routliers:::outliers_mcd.default(x = data.frame(SOC, HSC), na.rm = T)
   3.   └─Routliers:::outliers_mcdEst(x, h, alpha, na.rm)
   4.     └─stats::mahalanobis(data, output$center, output$cov)
   5.       └─base::sweep(x, 2L, center)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 2 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
royston.test: no visible global function definition for ‘shapiro.test’
royston.test: no visible global function definition for ‘cor’
royston.test: no visible global function definition for ‘qnorm’
royston.test: no visible global function definition for ‘pnorm’
royston.test: no visible global function definition for ‘cov’
royston.test: no visible global function definition for ‘mahalanobis’
royston.test: no visible global function definition for ‘qqplot’
royston.test: no visible global function definition for ‘qchisq’
royston.test: no visible global function definition for ‘ppoints’
royston.test: no visible global function definition for ‘abline’
royston.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  abline cor cov mahalanobis pchisq pnorm ppoints qchisq qnorm qqplot
  shapiro.test
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "cor", "cov", "mahalanobis", "pchisq", "pnorm",
             "ppoints", "qchisq", "qnorm", "qqplot", "shapiro.test")
to your NAMESPACE file.
Running examples in ‘royston-Ex.R’ failed
The error most likely occurred in:

> ### Name: royston.test
> ### Title: Royston's Multivariate Normality Test
> ### Aliases: royston.test
> 
> ### ** Examples
> 
> a=iris[1:50,1:4] # Iris data only for setosa and four variables
> royston.test(a)  # Data analyzed have a non-normal distribution.
Error in FUN(x, aperm(array(STATS, dims[perm]), order(perm)), ...) : 
  non-numeric argument to binary operator
Calls: royston.test -> mahalanobis -> sweep
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘tree’ in Rd xrefs
evalMedian: no visible global function definition for ‘xtabs’
evalMode: no visible global function definition for ‘xtabs’
rpartScore: no visible global function definition for ‘model.extract’
rpartScore: no visible global function definition for ‘var’
rpartScore: no visible binding for global variable ‘var’
splitAbs: no visible global function definition for ‘xtabs’
Undefined global functions or variables:
  model.extract var xtabs
Consider adding
  importFrom("stats", "model.extract", "var", "xtabs")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
'library' or 'require' call to ‘RODBC’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
rpart.rules.push: no visible global function definition for ‘sqlSave’
rpart.rules.table : <anonymous>: no visible global function definition
  for ‘setNames’
rpart.subrules.table : <anonymous>: no visible global function
  definition for ‘setNames’
Undefined global functions or variables:
  setNames sqlSave
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Non-standard file/directory found at top level:
  ‘Read-and-delete-me’
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘survival’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘MASS’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GenerateData: no visible global function definition for ‘mvrnorm’
GetVarImp : FitPenalizedModel: no visible global function definition
  for ‘clogit’
Undefined global functions or variables:
  clogit mvrnorm
Rd file 'GetVarImp.Rd':
  \examples lines wider than 100 characters:
     hist(MyResults, breaks=6, col="orange", xlab="Importance score", ylab="Number of features", main="Histogram of R-PCLR variable importan ... [TRUNCATED]
     ## Sort from most important (highest importance score) to least important feature (lowest importance score)

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘Rpdb.pdb’
Undeclared package ‘rsoi’ in Rd xrefs
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘mygraph.eps’ ‘mygraph.png’ ‘mygraph.tex’
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
Namespaces in Imports field not imported from:
  ‘SparseM’ ‘nlme’ ‘timeDate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘htmlwidgets’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Namespaces in Imports field not imported from:
  ‘ape’ ‘igraph’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Non-standard file/directory found at top level:
  ‘rpsychi-Ex.R’
Rd file 'ind.prop.Rd':
  \examples lines wider than 100 characters:
     ind.prop(y~x, data=dat, lev.count=2, ref.ind=1)    #Odds for not relapse is higher in treatment than control condition.
     ind.prop(y~x, data=dat, lev.count=1, ref.ind=1)    #Odds for relapse is lower in treatment than control condition.
     ind.prop(y~x, data=dat, lev.count=2, ref.ind=2)    #Odds for not relapse is lower in control than treatment condition.
     ind.prop(y~x, data=dat, lev.count=1, ref.ind=2)    #Odds for relapse is higher in control than treatment condition.

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

These lines will be truncated in the PDF manual.
Undeclared package ‘scalreg’ in Rd xrefs
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘HL_H0.pdf’ ‘pi0infer.pdf’ ‘rate.txt’ ‘summary.txt’
Namespace in Imports field not imported from: ‘NatureSounds’
  All declared Imports should be used.
Running examples in ‘rrcov-Ex.R’ failed
The error most likely occurred in:

> ### Name: T2.test
> ### Title: Robust Hotelling T2 test
> ### Aliases: T2.test T2.test.default T2.test.formula
> ### Keywords: htest multivariate
> 
> ### ** Examples
> 
> 
> ## One-sample classical test
> data(delivery)
> delivery.x <- delivery[,1:2]
> T2.test(delivery.x)
Error in .tomatrix(x) : x  is not a numeric dataframe or matrix.
Calls: T2.test -> T2.test.default -> .tomatrix
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘rrcov.Rnw’ using Sweave
Loading required package: robustbase
Scalable Robust Estimators with High Breakdown Point (version 1.6-0)


Error: processing vignette 'rrcov.Rnw' failed with diagnostics:
 chunk 13 (label = ex-cov-plot-lattice) 
Error in FUN(x, aperm(array(STATS, dims[perm]), order(perm)), ...) : 
  non-numeric argument to binary operator

--- failed re-building ‘rrcov.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    extdata  12.8Mb
‘configure’: ‘env bash’ is not portable as bash need not be installed
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.bpl’ ‘test.cr’ ‘test.ct’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘webshot2’
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.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘robustbase’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.computekappa: no visible global function definition for ‘pnorm’
.computekappa: no visible global function definition for ‘dnorm’
.initmethod : <anonymous>: no visible global function definition for
  ‘median’
.initmethod: no visible global function definition for ‘model.matrix’
.mspe: no visible global function definition for ‘rnorm’
.mspe : <anonymous>: no visible global function definition for ‘rnorm’
makedata: no visible global function definition for ‘rnorm’
makedata : addraneff: no visible global function definition for ‘rnorm’
plot.meanssaemodel: no visible global function definition for ‘par’
plot.meanssaemodel: no visible global function definition for ‘lines’
plot.meanssaemodel: no visible global function definition for ‘axis’
plot.meanssaemodel: no visible global function definition for ‘grid’
plot.meanssaemodel: no visible global function definition for ‘box’
plot.meanssaemodel: no visible global function definition for ‘legend’
plot.meanssaemodel: no visible global function definition for ‘arrows’
saemodel: no visible global function definition for ‘model.frame’
saemodel: no visible global function definition for ‘model.response’
saemodel: no visible global function definition for ‘model.matrix’
summary.fitsaemodel: no visible global function definition for ‘pt’
summary.fitsaemodel: no visible global function definition for
  ‘printCoefmat’
Undefined global functions or variables:
  arrows axis box dnorm grid legend lines median model.frame
  model.matrix model.response par pnorm printCoefmat pt rnorm
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "grid", "legend",
             "lines", "par")
  importFrom("stats", "dnorm", "median", "model.frame", "model.matrix",
             "model.response", "pnorm", "printCoefmat", "pt", "rnorm")
to your NAMESPACE file.
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.
Undeclared package ‘sp’ in Rd xrefs
stripslash: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lubridate’ ‘reshape2’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘keras’, ‘tensorflow’, ‘devtools’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
Imports includes 28 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘labelled’
  All declared Imports should be used.
convexhull: no visible global function definition for ‘chull’
convexhull: no visible global function definition for ‘rnorm’
drawcompletegraph: no visible global function definition for ‘segments’
getbag: no visible global function definition for ‘chull’
getbag: no visible global function definition for ‘polygon’
getbag: no visible global function definition for ‘points’
inflate: no visible global function definition for ‘rnorm’
rsmed: no visible global function definition for ‘runif’
rsplot: no visible global function definition for ‘chull’
rsplot: no visible global function definition for ‘polygon’
rsplot: no visible global function definition for ‘points’
rsrings: no visible global function definition for ‘chull’
rsrings: no visible global function definition for ‘polygon’
rsrings: no visible global function definition for ‘points’
rstinterval: no visible global function definition for ‘runif’
rstinterval: no visible global function definition for ‘rnorm’
rstinterval: no visible global function definition for ‘chull’
rstinterval: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  chull points polygon rnorm runif segments
Consider adding
  importFrom("grDevices", "chull")
  importFrom("graphics", "points", "polygon", "segments")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rcompression’
Namespaces in Imports field not imported from:
  ‘binman’ ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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)
  Found ‘stderr’, possibly from ‘stderr’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
addNoisyCopies: no visible global function definition for ‘rnorm’
eta: no visible global function definition for ‘var’
gaussClassifier: no visible global function definition for ‘runif’
getSigma: no visible global function definition for ‘sd’
getSigma: no visible binding for global variable ‘sd’
sfaClassify: no visible global function definition for ‘rainbow’
sfaClassify: no visible global function definition for ‘par’
sfaClassify: no visible global function definition for ‘points’
sfaClassify: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines par points rainbow rnorm runif sd var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "lines", "par", "points")
  importFrom("stats", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Running examples in ‘rSFA-Ex.R’ failed
The error most likely occurred in:

> ### Name: sfa2
> ### Title: The SFA2 algorithm, SFA with degree 2 expansion.
> ### Aliases: sfa2
> 
> ### ** Examples
> 
> ## prepare input data for simple demo
> t=seq.int(from=0,by=0.011,to=2*pi)
> x1=sin(t)+cos(11*t)^2
> x2=cos(11*t)
> x=data.frame(x1,x2)
> ## perform sfa2 algorithm with data
> res = sfa2(x)
[1] "Start preprocessing"
[1] "Close preprocessing"
[1] "Whitening and dimensionality reduction (PCA)"
[1] "Init expansion step"
[1] "Close expansion step"
[1] "Perform Slow Feature Analysis"
[1] "Using alternate [WisSej02] approach for SFA-calculation ..."
[1] "rank of B =  5"
[1] "epsC*lammax=  5.82188685724767e-09"
[1] "SFA2 closed"
Error in DATA - matrix(sfaList$avg0, customSize(DATA, 1), length(sfaList$avg0),  : 
  non-conformable arrays
Calls: sfa2 -> sfaExecute
Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs  13.2Mb
Note: found 467 marked UTF-8 strings
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘rsm-Ex.R’ failed
The error most likely occurred in:

> ### Name: coded.data
> ### Title: Functions for coded data
> ### Aliases: coded.data as.coded.data decode.data recode.data is.coded.data
> ###   val2code code2val print.coded.data [.coded.data codings
> ###   codings.coded.data codings<- names<-.coded.data truenames
> ###   truenames.coded.data truenames<- truenames<-.coded.data
> ### Keywords: regression design
> 
> ### ** Examples
> 
> library(rsm)
> 
> ### Existing dataset with variables on actual scale
> CR <- coded.data (ChemReact, x1 ~ (Time - 85)/5, x2 ~ (Temp - 175)/5)
> CR                            # same as print(CR, decode = TRUE)
    Time   Temp Block Yield
1  80.00 170.00    B1  80.5
2  80.00 180.00    B1  81.5
3  90.00 170.00    B1  82.0
4  90.00 180.00    B1  83.5
5  85.00 175.00    B1  83.9
6  85.00 175.00    B1  84.3
7  85.00 175.00    B1  84.0
8  85.00 175.00    B2  79.7
9  85.00 175.00    B2  79.8
10 85.00 175.00    B2  79.5
11 92.07 175.00    B2  78.4
12 77.93 175.00    B2  75.6
13 85.00 182.07    B2  78.5
14 85.00 167.93    B2  77.0

Data are stored in coded form using these coding formulas ...
x1 ~ (Time - 85)/5
x2 ~ (Temp - 175)/5
> print(CR, decode = FALSE)     # similar to as.data.frame(CR)
       x1     x2 Block Yield
1  -1.000 -1.000    B1  80.5
2  -1.000  1.000    B1  81.5
3   1.000 -1.000    B1  82.0
4   1.000  1.000    B1  83.5
5   0.000  0.000    B1  83.9
6   0.000  0.000    B1  84.3
7   0.000  0.000    B1  84.0
8   0.000  0.000    B2  79.7
9   0.000  0.000    B2  79.8
10  0.000  0.000    B2  79.5
11  1.414  0.000    B2  78.4
12 -1.414  0.000    B2  75.6
13  0.000  1.414    B2  78.5
14  0.000 -1.414    B2  77.0

Variable codings ...
x1 ~ (Time - 85)/5
x2 ~ (Temp - 175)/5
> code2val (c(x1=.5, x2=-1), codings = codings(CR))
Error in mode(expr) : node stack overflow
Calls: code2val ... paste -> deparse -> %in% -> mode -> deparse -> %in% -> mode
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘rs-illus.Rtex’ using Sweave
--- finished re-building ‘rs-illus.Rtex’

--- re-building ‘rsm-plots.Rtex’ using Sweave
Warning in title(sub = dat$labs[5], ...) :
  "shade" is not a graphical parameter
--- finished re-building ‘rsm-plots.Rtex’

--- re-building ‘rsm.Rtex’ using Sweave

Error: processing vignette 'rsm.Rtex' failed with diagnostics:
 chunk 5 
Error : node stack overflow

--- failed re-building ‘rsm.Rtex’

SUMMARY: processing the following file failed:
  ‘rsm.Rtex’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘h2o’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Namespace in Imports field not imported from: ‘MatrixExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 41.3Mb
  sub-directories of 1Mb or more:
    libs  40.7Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
negbin.pow : negbin.disp: no visible global function definition for
  ‘rpois’
negbin.pow : negbin.disp: no visible global function definition for
  ‘rnbinom’
negbin.pow : inner.fcn: no visible global function definition for
  ‘na.omit’
negbin.pow : inner.fcn: no visible global function definition for
  ‘quantile’
negbin.pow: no visible global function definition for ‘txtProgressBar’
negbin.pow: no visible global function definition for
  ‘setTxtProgressBar’
poiss.pow : inner.fcn: no visible global function definition for
  ‘rpois’
poiss.pow : inner.fcn: no visible global function definition for
  ‘quantile’
poiss.pow: no visible global function definition for ‘txtProgressBar’
poiss.pow: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  na.omit quantile rnbinom rpois setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "quantile", "rnbinom", "rpois")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Database’ ‘rSQM.yaml’ ‘rSQM_Sample_Project’ ‘sample_script.R’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 194.7Mb
  sub-directories of 1Mb or more:
    R       1.6Mb
    doc     4.5Mb
    libs  188.0Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
Undeclared packages ‘gamm4’, ‘shiny’, ‘biglm’ in Rd xrefs
GNU make is a SystemRequirements.
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    libs  23.4Mb
GNU make is a SystemRequirements.
Running ‘spelling.R’
  Running ‘testthat.R’ [40s/51s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rstanemax)
  Loading required package: Rcpp
  > 
  > # options(lifecycle_verbosity = "error")
  > test_check("rstanemax")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-posterior_predict.R:68:3): posterior prediction with new data with covariates ──
  Error in `check_covs_in_data(data, param.cov)`: Covariate specified with `param.cov` does not exist in the dataset
  Backtrace:
      █
   1. └─rstanemax:::posterior_predict.stanemax(...) test-posterior_predict.R:68:2
   2.   └─rstanemax:::create_model_frame(...)
   3.     └─rstanemax:::check_covs_in_data(data, param.cov)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 58 ]
  Error: Test failures
  Execution halted
installed size is 193.9Mb
  sub-directories of 1Mb or more:
    lib    27.7Mb
    libs  163.4Mb
Undeclared packages ‘coda’, ‘rstanarm’ in Rd xrefs
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
Running ‘testthat.R’ [4m/12m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(RStoolbox) 
  > 
  > 
  > Sys.setenv("R_TESTS" = "") ## needed to pass R CMD check: https://github.com/hadley/testthat/issues/144
  > 
  > test_check("RStoolbox")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (11)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-sam.R:30:13): endmember class ───────────────────────────────────
  <Rcpp::not_compatible/C++Error/error/condition>
  Error in `specSimC(x = xi, em = emc)`: Not compatible with requested type: [type=list; target=double].
  Backtrace:
       █
    1. ├─testthat::expect_is(ls <- sam(lsat, sem_df, angles = TRUE), "RasterBrick") test-sam.R:30:12
    2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. └─RStoolbox::sam(lsat, sem_df, angles = TRUE)
    5.   ├─raster::calc(...)
    6.   └─raster::calc(...)
    7.     └─raster:::.local(x, fun, ...)
    8.       └─raster:::.calcTest(x[1:5], fun, na.rm, forcefun, forceapply)
    9.         └─RStoolbox:::fun(tstdat)
   10.           └─RStoolbox:::specSimC(x = xi, em = emc)
  
  [ FAIL 1 | WARN 41 | SKIP 11 | PASS 555 ]
  Error: Test failures
  Execution halted
Running examples in ‘RStorm-Ex.R’ failed
The error most likely occurred in:

> ### Name: GetTrack
> ### Title: Function to retrieve objects stored using the 'SetTrack'
> ###   functionality during a stream.
> ### Aliases: GetTrack
> ### Keywords: utilities programming
> 
> ### ** Examples
> 
> 
> # Create a topology with a spout
> topology <- Topology(data.frame(x=c(1:10)))
Created a topology with a spout containing  10 rows.> 
> # Add a bolt to the topology
> computeSum <- function(x, ...){
+ 	sum <- GetHash("sum")
+ 	if(is.data.frame(sum)){
+ 		x <- sum + (x[1])
+ 	}
+ 	SetHash("sum", x)
+ 	# Track the current state during the stream:
+ 	TrackRow("sum", data.frame(x=x))
+ }
> topology <- AddBolt(topology, Bolt(computeSum))
[1] "Added bolt computeSum to position 1 which listens to 0"
> 
> # Run the stream
> result <- RStorm(topology)
Warning in `[.data.frame`(x$env$data, 1L, drop = FALSE) :
  'drop' argument will be ignored
Error in TrackRow("sum", data.frame(x = x)) : 
  Tracked rows should be a single row dataframe
Calls: RStorm ... llply -> loop_apply -> <Anonymous> -> .fun -> TrackRow
Execution halted
Note: found 117 marked UTF-8 strings
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
Undeclared package ‘flexsurv’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘bitops’ ‘httpuv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mc2d’
  All declared Imports should be used.
Note: found 18627 marked UTF-8 strings
Found the following files/directories:
  ‘mapCH2017.rda’
Undeclared packages ‘lpSolve’, ‘Rglpk’ in Rd xrefs
Undeclared package ‘spacyr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R           1.2Mb
    bootstrap   1.6Mb
    data        2.2Mb
Malformed Title field: should not end in a period.
barplot.rtconnect: no visible global function definition for ‘rainbow’
barplot.rtconnect: no visible global function definition for ‘text’
plot.rtconnect: no visible global function definition for ‘par’
plot.rtconnect: no visible global function definition for ‘axis.Date’
rtconnect: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  axis.Date par rainbow read.table text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis.Date", "par", "text")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Running examples in ‘R.temis-Ex.R’ failed
The error most likely occurred in:

> ### Name: add_clusters
> ### Title: add_clusters
> ### Aliases: add_clusters
> 
> ### ** Examples
> 
> 
> file <- system.file("texts", "reut21578-factiva.xml", package="tm.plugin.factiva")
> corpus <- import_corpus(file, "factiva", language="en")
> dtm <- build_dtm(corpus)
> res <- corpus_ca(corpus, dtm, ncp=2, sparsity=0.98)
> clust <- corpus_clustering(res, 3)
Error in is.table(X) : object 'newDtm' not found
Calls: corpus_clustering ... as.data.frame.list -> do.call -> <Anonymous> -> <Anonymous> -> is.table
Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘stats’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
File ‘RTextTools/libs/RTextTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
plotGLCM: no visible global function definition for ‘points’
Undefined global functions or variables:
  points
Consider adding
  importFrom("graphics", "points")
to your NAMESPACE file.
Found the following files/directories:
  ‘test_addPageBreak.doc’ ‘test_addPlot.doc’ ‘test_addSessionInfo.doc’
  ‘test_addTable.doc’
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘httr’ ‘logger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    rmarkdown   5.8Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘stringr’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘MASS’ ‘gridExtra’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.6Mb
    projects   2.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Note: found 633 marked UTF-8 strings
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data      3.4Mb
    extdata   1.4Mb
    libs      3.3Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘RcppProgress’
  All declared Imports should be used.
Running ‘testthat.R’ [16s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(rTLS)
  Loading required package: data.table
  
  Attaching package: 'rTLS'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("rTLS")
  Number of threads=1
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  Number of threads=1
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-filter.R:11:3): Whether filter SOR works ──────────────────────
  nrow(to_SOR) (`actual`) not equal to 64777 (`expected`).
  
    `actual`: 64779
  `expected`: 64777
  Number of points
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 138 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘memoise’ ‘tidyr’
  All declared Imports should be used.
Note: found 37 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  17.6Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘RQuantLib’
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Tsttwalk.dat’
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Note: found 113868 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.1Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘ruler-Ex.R’ failed
The error most likely occurred in:

> ### Name: act_after_exposure
> ### Title: Act after exposure
> ### Aliases: act_after_exposure
> 
> ### ** Examples
> 
> exposure_printer <- function(.tbl) {
+   print(get_exposure(.tbl))
+   .tbl
+ }
> mtcars_exposed <- mtcars %>%
+   expose(data_packs(. %>% dplyr::summarise(nrow_low = nrow(.) > 50))) %>%
+   act_after_exposure(any_breaker, exposure_printer)
Error: The `x` argument to `enframe()` must be a vector, not tbl_df.
Backtrace:
     █
  1. ├─`%>%`(...)
  2. ├─ruler::act_after_exposure(., any_breaker, exposure_printer)
  3. │ └─ruler::get_exposure(.tbl)
  4. │   └─ruler::is_exposure(.object)
  5. ├─ruler::expose(...)
  6. │ └─.tbl %>% unkey() %>% use_id()
  7. └─keyholder::use_id(.)
  8.   └─keyholder::assign_keys(.tbl, tibble(.id = seq_len(nrow(.tbl))))
  9.     └─keyholder::`keys<-`(`*tmp*`, value = value)
 10.       └─tibble::enframe(value, name = NULL, value = "value")
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > library(rlang)
  
  Attaching package: 'rlang'
  
  The following objects are masked from 'package:testthat':
  
      is_false, is_null, is_true
  
  > library(ruler)
  > 
  > test_check("ruler")
  Error: The `x` argument to `enframe()` must be a vector, not tbl_df.
  Backtrace:
       █
    1. ├─testthat::test_check("ruler")
    2. │ └─testthat::test_dir(...)
    3. │   └─testthat:::test_files(...)
    4. │     └─testthat:::test_files(...)
    5. │       └─testthat:::test_files_setup_state(...)
    6. │         └─testthat::source_test_helpers(".", env)
    7. │           └─testthat::source_dir(path, "^helper.*\\.[rR]$", env = env, wrap = FALSE)
    8. │             └─base::lapply(files, source_file, env = env, chdir = chdir, wrap = wrap)
    9. │               └─testthat:::FUN(X[[i]], ...)
   10. │                 └─base::eval(exprs, env)
   11. │                   └─base::eval(exprs, env)
   12. │                     └─`%>%`(...) helper-expose-data.R:12:0
   13. └─keyholder::assign_keys(., tibble::tibble(.id = c(1, 3)))
   14.   └─keyholder::`keys<-`(`*tmp*`, value = value)
   15.     └─tibble::enframe(value, name = NULL, value = "value")
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘design-and-format.Rmd’ using rmarkdown
--- finished re-building ‘design-and-format.Rmd’

--- re-building ‘rule-packs.Rmd’ using rmarkdown
--- finished re-building ‘rule-packs.Rmd’

--- re-building ‘validation.Rmd’ using rmarkdown
Quitting from lines 91-94 (validation.Rmd) 
Error: processing vignette 'validation.Rmd' failed with diagnostics:
The `x` argument to `enframe()` must be a vector, not tbl_df.
--- failed re-building ‘validation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘rmarkdown’ ‘table1’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘results’
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Rd file 'Runiversal-package.Rd':
  \examples lines wider than 100 characters:
     #Getting estimates from regression object as Java variables that be directly interpretable by Bean Shell.

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘somefile.xml’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 45.4Mb
  sub-directories of 1Mb or more:
    libs  44.7Mb
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘XML’
  All declared Imports should be used.
installed size is 51.1Mb
  sub-directories of 1Mb or more:
    libs  49.9Mb
Running examples in ‘Rvcg-Ex.R’ failed
The error most likely occurred in:

> ### Name: vcgKmeans
> ### Title: fast Kmean clustering for 1D, 2D and 3D data
> ### Aliases: vcgKmeans
> 
> ### ** Examples
> 
> require(Rvcg);require(rgl)
Loading required package: rgl
> data(humface)
> set.seed(42)
> clust <- vcgKmeans(humface,k=1000,threads=1)
Error in vcgKmeans(humface, k = 1000, threads = 1) : 
  number of centers exceeds sample size
Execution halted
Found the following files/directories:
  ‘humface.ply’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
HapMendlianCheck: no visible global function definition for
  ‘write.table’
rvPDT.test.sub: no visible global function definition for ‘pnorm’
whap.prehap: no visible global function definition for ‘write.table’
whap.prehap: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  pnorm read.table write.table
Consider adding
  importFrom("stats", "pnorm")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
'library' or 'require' call to ‘pixmap’ which was already attached by Depends.
  Please remove these calls from your code.
rvideopoker: warning in rp.radiogroup(mypanel, var =
  state$penny.nickel.quarter.dollar, initval = 1, values = c(1, 5, 25,
  100), title = "Bet (in Cents)", action = setbet): partial argument
  match of 'var' to 'variable'
rvideopoker: warning in rp.slider(mypanel, var = state$no.of.credits,
  from = 1, to = 5, initval = 1, title = "How many Credits?",
  resolution = 1, action = creditset, showvalue = TRUE): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC1, action = card1check, title = "Keep Card 1?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC2, action = card2check, title = "Keep Card 2?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC3, action = card3check, title = "Keep Card 3?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC4, action = card4check, title = "Keep Card 4?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC5, action = card5check, title = "Keep Card 5?"): partial
  argument match of 'var' to 'variable'
rvideopoker : plotFrame: no visible global function definition for
  ‘par’
rvideopoker : showBack: no visible global function definition for
  ‘title’
rvideopoker : showCardsInitially: no visible global function definition
  for ‘title’
Undefined global functions or variables:
  par title
Consider adding
  importFrom("graphics", "par", "title")
to your NAMESPACE file.
Package suggested but not available for checking: ‘gpuR’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    include   5.3Mb
installed size is 54.0Mb
  sub-directories of 1Mb or more:
    include   5.0Mb
    libs     48.6Mb
Undeclared package ‘wdm’ in Rd xrefs
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-clang/RVowpalWabbit.Rcheck/00install.out’ for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
    test   4.5Mb
Malformed Description field: should contain one or more complete sentences.
lc_TDT: no visible global function definition for ‘pchisq’
rvTDT: no visible global function definition for ‘dbeta’
Undefined global functions or variables:
  dbeta pchisq
Consider adding
  importFrom("stats", "dbeta", "pchisq")
to your NAMESPACE file.
LASSO: no visible global function definition for ‘lm’
LASSO: no visible global function definition for ‘anova’
LASSO: no visible global function definition for ‘glm’
LASSO: no visible global function definition for ‘pchisq’
LASSO : <anonymous>: no visible global function definition for
  ‘extractAIC’
PCR : <anonymous>: no visible global function definition for ‘cor’
PLS : <anonymous>: no visible global function definition for ‘cor’
RR : RRscore: no visible binding for global variable ‘sd’
SPLS: no visible global function definition for ‘lm’
SPLS: no visible global function definition for ‘anova’
SPLS : <anonymous>: no visible global function definition for
  ‘extractAIC’
VTWOD : getScores: no visible global function definition for ‘sd’
VTWOD : getScores: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  anova cor extractAIC glm lm pchisq pnorm sd
Consider adding
  importFrom("stats", "anova", "cor", "extractAIC", "glm", "lm",
             "pchisq", "pnorm", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
check_ISO_code: no visible binding for global variable ‘NoAm_country’
check_ISO_code: no visible binding for global variable ‘SoAm_country’
check_ISO_code: no visible binding for global variable ‘Oceana_country’
check_ISO_code: no visible binding for global variable ‘Africa_country’
check_ISO_code: no visible binding for global variable ‘Asia_country’
check_ISO_code: no visible binding for global variable ‘Eur_country’
climate_map: no visible binding for global variable ‘data’
date_correct: no visible global function definition for ‘tail’
Undefined global functions or variables:
  Africa_country Asia_country Eur_country NoAm_country Oceana_country
  SoAm_country data tail
Consider adding
  importFrom("utils", "data", "tail")
to your NAMESPACE file.
RWBP.default: no visible global function definition for ‘na.omit’
RWBP.default: no visible global function definition for ‘kmeans’
RWBP.formula: no visible global function definition for ‘model.extract’
predict.RWBP: no visible global function definition for ‘head’
Undefined global functions or variables:
  head kmeans model.extract na.omit
Consider adding
  importFrom("stats", "kmeans", "model.extract", "na.omit")
  importFrom("utils", "head")
to your NAMESPACE file.
weblogo: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
Found the following files/directories:
  ‘RWebLogo.pdf’ ‘RWebLogo.png’
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
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.
Note: found 4250 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
File
  LICENSE
is not mentioned in the DESCRIPTION file.
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Undeclared package ‘tm’ in Rd xrefs
Note: found 2016 marked UTF-8 strings
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Malformed Title field: should not end in a period.
Note: found 426306 marked UTF-8 strings
.dwt: no visible global function definition for ‘median’
.udwt: no visible global function definition for ‘median’
plotSignalTransformation: no visible global function definition for
  ‘box’
plotSignalTransformation: no visible global function definition for
  ‘axis’
plotSignalTransformation: no visible global function definition for
  ‘lines’
plotSignalTransformation: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  axis box legend lines median
Consider adding
  importFrom("graphics", "axis", "box", "legend", "lines")
  importFrom("stats", "median")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
installed size is 48.5Mb
  sub-directories of 1Mb or more:
    libs  45.8Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs    6.1Mb
    yacas   1.5Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs    6.6Mb
    yacas   1.6Mb
Undeclared package ‘rym’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Undeclared package ‘jsonlite’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    libs  34.3Mb
Namespace in Imports field not imported from: ‘spanel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
calculate.summary: no visible global function definition for ‘sd’
detect.saccades: no visible global function definition for ‘median’
diagnostic.plot: no visible global function definition for ‘dev.new’
diagnostic.plot: no visible global function definition for ‘par’
diagnostic.plot: no visible global function definition for ‘recordPlot’
diagnostic.plot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.new dev.off median par recordPlot sd
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "recordPlot")
  importFrom("graphics", "par")
  importFrom("stats", "median", "sd")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘R6’ ‘mgcv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
fit.saery.AR1: no visible global function definition for ‘qnorm’
fit.saery.MA1: no visible global function definition for ‘qnorm’
fit.saery.indep: no visible global function definition for ‘qnorm’
mse.saery.boot.AR1.typeI: no visible global function definition for
  ‘rnorm’
mse.saery.boot.AR1.typeI: no visible global function definition for
  ‘write.table’
mse.saery.boot.AR1.typeII: no visible global function definition for
  ‘rnorm’
mse.saery.boot.AR1.typeII: no visible global function definition for
  ‘write.table’
mse.saery.boot.MA1.typeI: no visible global function definition for
  ‘rnorm’
mse.saery.boot.MA1.typeI: no visible global function definition for
  ‘write.table’
mse.saery.boot.MA1.typeII: no visible global function definition for
  ‘rnorm’
mse.saery.boot.MA1.typeII: no visible global function definition for
  ‘write.table’
plot.saery: no visible global function definition for ‘devAskNewPage’
plot.saery: no visible global function definition for ‘par’
plot.saery: no visible global function definition for ‘abline’
plot.saery: no visible global function definition for ‘title’
plot.saery: no visible global function definition for ‘axis’
plot.saery: no visible global function definition for ‘lines’
plot.saery: no visible global function definition for ‘legend’
pvalue: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline axis devAskNewPage legend lines par pnorm qnorm rnorm title
  write.table
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "title")
  importFrom("stats", "pnorm", "qnorm", "rnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Undeclared packages ‘magrittr’, ‘rlang’ in Rd xrefs
Package in Depends field not imported from: ‘lpSolveAPI’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
glm: no visible binding for global variable ‘gaussian’
glm: no visible global function definition for ‘glm.control’
glm: no visible global function definition for ‘model.response’
glm: no visible global function definition for ‘is.empty.model’
glm: no visible global function definition for ‘model.matrix’
glm: no visible global function definition for ‘model.weights’
glm: no visible global function definition for ‘model.offset’
glm: no visible global function definition for ‘model.extract’
glm: no visible global function definition for ‘glm.fit’
glm: no visible global function definition for ‘.getXlevels’
separator: no visible global function definition for ‘make.lp’
separator: no visible global function definition for ‘set.column’
separator: no visible global function definition for ‘set.rhs’
separator: no visible global function definition for ‘set.constr.type’
separator: no visible global function definition for ‘set.objfn’
separator: no visible global function definition for ‘set.bounds’
separator: no visible global function definition for ‘lp.control’
separator: no visible global function definition for ‘get.variables’
separator: no visible global function definition for ‘set.basis’
separator: no visible global function definition for
  ‘get.dual.solution’
Undefined global functions or variables:
  .getXlevels gaussian get.dual.solution get.variables glm.control
  glm.fit is.empty.model lp.control make.lp model.extract model.matrix
  model.offset model.response model.weights set.basis set.bounds
  set.column set.constr.type set.objfn set.rhs
Consider adding
  importFrom("stats", ".getXlevels", "gaussian", "glm.control",
             "glm.fit", "is.empty.model", "model.extract",
             "model.matrix", "model.offset", "model.response",
             "model.weights")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’
  All declared Imports should be used.
Note: found 3 marked Latin-1 strings
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘safetyCharts’
  All declared Imports should be used.
Note: found 91 marked UTF-8 strings
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.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [22s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(salty)
  > 
  > test_check("salty")
  
  Attaching package: 'purrr'
  
  The following object is masked from 'package:testthat':
  
      is_null
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-utils.R:4:3): p_indices rejects invalid inputs ────────────────
  `p_indices(iris, 0.2)` did not throw an error.
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 824 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs  13.3Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
'LazyData' is specified without a 'data' directory
Rd file 'mudiff.acc.Rd':
  \usage lines wider than 90 characters:
     mudiff.acc(len, alpha1, beta1, alpha2, beta2, n01, n02, level = 0.95, equal = TRUE, m = 10000, mcs = 3)

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

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

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

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

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

These lines will be truncated in the PDF manual.
propdiff.acc: no visible global function definition for ‘rbeta’
propdiff.acc: no visible global function definition for ‘rbinom’
propdiff.acc: no visible global function definition for ‘pbeta’
propdiff.alc: no visible global function definition for ‘rbeta’
propdiff.alc: no visible global function definition for ‘rbinom’
propdiff.alc: no visible global function definition for ‘qbeta’
propdiff.freq: no visible global function definition for ‘qnorm’
propdiff.mblacc: no visible global function definition for ‘rbeta’
propdiff.mblacc: no visible global function definition for ‘rbinom’
propdiff.mblacc: no visible global function definition for ‘pbeta’
propdiff.mblalc: no visible global function definition for ‘rbeta’
propdiff.mblalc: no visible global function definition for ‘rbinom’
propdiff.mblalc: no visible global function definition for ‘qbeta’
propdiff.mblmodwoc: no visible global function definition for ‘qchisq’
propdiff.mblmodwoc: no visible global function definition for ‘pbeta’
propdiff.mblwoc: no visible global function definition for ‘pbeta’
propdiff.modwoc: no visible global function definition for ‘qchisq’
propdiff.modwoc: no visible global function definition for ‘pbeta’
propdiff.woc: no visible global function definition for ‘pbeta’
Undefined global functions or variables:
  pbeta qbeta qchisq qnorm rbeta rbinom
Consider adding
  importFrom("stats", "pbeta", "qbeta", "qchisq", "qnorm", "rbeta",
             "rbinom")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs  24.2Mb
GraphBinaryForestPlot: no visible global function definition for
  ‘abline’
GraphBinaryForestPlot: no visible global function definition for ‘text’
GraphContinuousForestPlot: no visible global function definition for
  ‘abline’
GraphContinuousForestPlot: no visible global function definition for
  ‘text’
ImputeBinaryEvents: no visible global function definition for ‘rbinom’
ImputeSMD: no visible global function definition for ‘rnorm’
funnelplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline rbinom rnorm text
Consider adding
  importFrom("graphics", "abline", "text")
  importFrom("stats", "rbinom", "rnorm")
to your NAMESPACE file.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   3.1Mb
generate.sample.core: no visible global function definition for
  ‘predict’
mdh: no visible global function definition for ‘model.frame’
mdh: no visible binding for global variable ‘na.fail’
mdh: no visible global function definition for ‘.getXlevels’
mdh: no visible global function definition for ‘quantile’
mdh: no visible global function definition for ‘hist’
predict.mdh: no visible global function definition for ‘model.frame’
samur: no visible global function definition for ‘predict’
Undefined global functions or variables:
  .getXlevels hist model.frame na.fail predict quantile
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", ".getXlevels", "model.frame", "na.fail", "predict",
             "quantile")
to your NAMESPACE file.
Note: found 6 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Running examples in ‘sarima-Ex.R’ failed
The error most likely occurred in:

> ### Name: acfGarchTest
> ### Title: Test for GARCH white noise
> ### Aliases: acfGarchTest acfWnTest
> ### Keywords: ts garch htest
> 
> ### ** Examples
> 
> ## see also the examples for \code{whiteNoiseTest}
> n <- 5000
> x <- sarima:::rgarch1p1(n, alpha = 0.3, beta = 0.55, omega = 1, n.skip = 100)
> x.acf <- autocorrelations(x)
Error in validObject(.Object) : 
  invalid class “Lagged1d” object: invalid object for slot "data" in class "Lagged1d": got class "acf", should be or extend class "vector"
Calls: autocorrelations ... Lagged -> new -> initialize -> initialize -> validObject
Execution halted
Running ‘testthat.R’ [230s/296s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > ## Sys.setenv(R_TESTS="")
  > library(testthat)
  > library(sarima)
  Loading required package: stats4
  > 
  > test_check("sarima")
  An object of class "SarimaModel"
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-autocovariances.R:13:5): functions in autocorrelations.org work ok ──
  Error in `validObject(.Object)`: invalid class "Lagged1d" object: invalid object for slot "data" in class "Lagged1d": got class "acf", should be or extend class "vector"
  Backtrace:
      █
   1. ├─sarima::autocorrelations(v1) test-autocovariances.R:13:4
   2. └─sarima::autocorrelations(v1)
   3.   └─sarima:::.basecfclass2S4(wrk)
   4.     └─lagged::Lagged(x)
   5.       └─methods::new("Lagged1d", data = data, ...)
   6.         ├─methods::initialize(value, ...)
   7.         └─methods::initialize(value, ...)
   8.           └─methods::validObject(.Object)
  ── Error (test-sarima.R:135:5): sarima() works ok ──────────────────────────────
  Error in `validObject(.Object)`: invalid class "Lagged1d" object: invalid object for slot "data" in class "Lagged1d": got class "acf", should be or extend class "vector"
  Backtrace:
       █
    1. ├─stats::tsdiag(ap.baseA) test-sarima.R:135:4
    2. └─sarima::tsdiag.Sarima(ap.baseA)
    3.   ├─sarima::autocorrelations(err, maxlag = nlag)
    4.   └─sarima::autocorrelations(err, maxlag = nlag)
    5.     └─sarima:::.basecfclass2S4(wrk)
    6.       └─lagged::Lagged(x)
    7.         └─methods::new("Lagged1d", data = data, ...)
    8.           ├─methods::initialize(value, ...)
    9.           └─methods::initialize(value, ...)
   10.             └─methods::validObject(.Object)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 181 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘garch_tests_example.Rnw’ using Sweave
Loading required package: stats4
Loading required package: timeDate
Loading required package: timeSeries
Loading required package: fBasics

Error: processing vignette 'garch_tests_example.Rnw' failed with diagnostics:
 chunk 5 
Error in validObject(.Object) : 
  invalid class “Lagged1d” object: invalid object for slot "data" in class "Lagged1d": got class "acf", should be or extend class "vector"

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

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

Error: processing vignette 'white_noise_tests.Rnw' failed with diagnostics:
 chunk 3 
Error in validObject(.Object) : 
  invalid class “Lagged1d” object: invalid object for slot "data" in class "Lagged1d": got class "acf", should be or extend class "vector"

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

SUMMARY: processing the following files failed:
  ‘garch_tests_example.Rnw’ ‘white_noise_tests.Rnw’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 42.0Mb
  sub-directories of 1Mb or more:
    bin  41.2Mb
download.sas7bdat.sources : <anonymous>: no visible global function
  definition for ‘download.file’
generate.sas7bdat.source: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
parse.SAScii: no visible binding for global variable ‘end’
parse.SAScii: no visible binding for global variable ‘start’
read.SAScii: no visible global function definition for ‘download.file’
read.SAScii: no visible global function definition for ‘unzip’
read.SAScii: no visible global function definition for ‘read.fwf’
read.SAScii: no visible global function definition for ‘capture.output’
Undefined global functions or variables:
  capture.output download.file end read.fwf start unzip
Consider adding
  importFrom("stats", "end", "start")
  importFrom("utils", "capture.output", "download.file", "read.fwf",
             "unzip")
to your NAMESPACE file.
Rd file 'read.SAScii.Rd':
  \usage lines wider than 90 characters:
     read.SAScii( fn, sas_ri, beginline = 1, buffersize = 50, zipped = F , n = -1 , intervals.to.print = 1000 , lrecl = NULL , skip.decimal. ... [TRUNCATED]
  \examples lines wider than 100 characters:
                     paste( "http://smpbff2.dsd.census.gov/pub/sipp/2004/l04puw" , i , ".zip" , sep = "" )

These lines will be truncated in the PDF manual.
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
SASPECT: no visible global function definition for ‘dbinom’
my.SOnePro: missing arguments not allowed in calls to ‘c’
my.ttest: no visible global function definition for ‘var’
Undefined global functions or variables:
  dbinom var
Consider adding
  importFrom("stats", "dbinom", "var")
to your NAMESPACE file.
Found the following files/directories:
  ‘SASPECT.result.txt’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘maptools’
  All declared Imports should be used.
Found the following files/directories:
  ‘stateLung-R01.pdf’ ‘stateLung-R01.txt’
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.
'LazyData' is specified without a 'data' directory
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.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
loads: no visible global function definition for ‘untar’
saves: no visible global function definition for ‘tar’
Undefined global functions or variables:
  tar untar
Consider adding
  importFrom("utils", "tar", "untar")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
K: no visible global function definition for ‘dnorm’
sBF: no visible global function definition for ‘density’
sBF: no visible global function definition for ‘txtProgressBar’
sBF: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  density dnorm setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "density", "dnorm")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘network’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   3.8Mb
Malformed Title field: should not end in a period.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Malformed Description field: should contain one or more complete sentences.
fitSBSA: no visible binding for global variable ‘var’
fitSBSA: no visible global function definition for ‘var’
fitSBSA: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm var
Consider adding
  importFrom("stats", "qnorm", "var")
to your NAMESPACE file.
File ‘SBSA/libs/SBSA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Non-standard file/directory found at top level:
  ‘src-java’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pvclust’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Undeclared package ‘plyr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.scair: no visible global function definition for ‘par’
plot.scair: no visible global function definition for ‘points’
plot.scar: no visible global function definition for ‘par’
plot.scar: no visible global function definition for ‘points’
predict.scair: no visible global function definition for ‘approx’
predict.scar: no visible global function definition for ‘approx’
scair: no visible global function definition for ‘gaussian’
scair: no visible global function definition for ‘runif’
scair: no visible global function definition for ‘rnorm’
scar: no visible global function definition for ‘gaussian’
scar: no visible global function definition for ‘glm.fit’
scar: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx gaussian glm.fit par points rnorm runif
Consider adding
  importFrom("graphics", "par", "points")
  importFrom("stats", "approx", "gaussian", "glm.fit", "rnorm", "runif")
to your NAMESPACE file.
Undeclared packages ‘Iso’, ‘scam’, ‘gam’ in Rd xrefs
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.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Running examples in ‘scclust-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_clustering_stats
> ### Title: Get clustering statistics
> ### Aliases: get_clustering_stats
> 
> ### ** Examples
> 
> my_data_points <- data.frame(x = c(0.1, 0.2, 0.3, 0.4, 0.5,
+                                    0.6, 0.7, 0.8, 0.9, 1.0),
+                              y = c(10, 9, 8, 7, 6,
+                                    10, 9, 8, 7, 6))
> 
> my_distances <- distances(my_data_points)
Error in distances(data = my_data_points) : `data` must be numeric.
Calls: distances -> coerce_distance_data -> new_error
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    libs   2.4Mb
Running examples in ‘scdhlm-Ex.R’ failed
The error most likely occurred in:

> ### Name: compare_RML_HPS
> ### Title: Run simulation comparing REML and HPS estimates
> ### Aliases: compare_RML_HPS
> 
> ### ** Examples
> 
> compare_RML_HPS(iterations=10, beta = c(0,1,0,0), rho = 0.3, 
+                  phi = 0.5, design=design_matrix(m=3,n=8))
Warning: 'g_REML()' is deprecated and may be removed in a later version of the package. Please use 'g_mlm()' instead.
Error in rep(phi^2, n - 2) : invalid 'times' argument
Calls: compare_RML_HPS ... tapply -> lapply -> FUN -> FUN -> AR1_corr_inv -> diag
Execution halted
Namespaces in Imports field not imported from:
  ‘future’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mathjaxr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘SCEPtERbinary/libs/SCEPtERbinary.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
prime.factor: no visible global function definition for ‘data’
prime.factor: no visible binding for global variable ‘primlist’
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘schoolmath/R/prime.factor.R’:
  data(primlist)
See section ‘Good practice’ in ‘?data’.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘stringi’ ‘stringr’ ‘tibble’ ‘tidyr’ ‘tidytext’
  All declared Imports should be used.
Note: found 464 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'simplifyEnrichment', 'conos', 'pagoda2'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [23s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sclr)
  > 
  > test_check("sclr")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-utilities.R:41:3): symmetrical matrix is created ──────────────
  build_symm_mat(vecs) not equal to `expected_out`.
  names for current but not for target
  Attributes: < names for target but not for current >
  Attributes: < Length mismatch: comparison on first 0 components >
  Length mismatch: comparison on first 2 components
  Component 1: Lengths: 2, 4
  Component 1: Attributes: < target is NULL, current is list >
  Component 1: target is numeric, current is matrix
  Component 2: Lengths: 2, 4
  Component 2: Attributes: < target is NULL, current is list >
  ...
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 86 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘BiocSingular’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
score.GGUM: no visible global function definition for ‘dnorm’
score.GGUM: no visible global function definition for ‘hist’
score.GGUM: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  dnorm hist write.table
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "dnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘EAP_est1.txt’
'LazyData' is specified without a 'data' directory
CreatePssm: no visible binding for global variable ‘training’
Undefined global functions or variables:
  training
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pracma’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running examples in ‘ScottKnott-Ex.R’ failed
The error most likely occurred in:

> ### Name: SK
> ### Title: The SK Test for Single Experiments
> ### Aliases: SK SK.default SK.aov SK.lm SK.formula SK.aovlist SK.lmerMod
> ### Keywords: package
> 
> ### ** Examples
> 
> ##
> ## Examples:Randomized Complete Block Design (RCBD)
> ## More details: demo(package='SK')
> ##
> 
> ## The parameters can be: formula, aov, lm, aovlist and lmerMod
> 
> data(RCBD)
> 
> ## From: formula
> sk1 <- with(RCBD,
+             SK(y ~ blk + tra,
+                data=dfm,
+                which='tra'))
Error in is.finite(x) : default method not implemented for type 'list'
Calls: with ... with.default -> eval -> eval -> SK -> SK.formula -> SK -> SK.lm
Execution halted
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  ‘RCurl’ ‘XML’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RCurl’ ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
scrape: no visible global function definition for ‘getURLAsynchronous’
scrape: no visible global function definition for ‘runif’
scrape: no visible global function definition for ‘capture.output’
scrape: no visible binding for global variable ‘xmlParse’
scrape: no visible binding for global variable ‘htmlParse’
Undefined global functions or variables:
  capture.output getURLAsynchronous htmlParse runif xmlParse
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘crayon’ ‘knitr’ ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘untitled_consensus_cluster’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘methods’ ‘pbapply’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘glmGamPoi’
'LazyData' is specified without a 'data' directory
lahiri.design: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘spatstat’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Note: found 51 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Running examples in ‘sdcMicro-Ex.R’ failed
The error most likely occurred in:

> ### Name: LocalRecProg
> ### Title: Local recoding via Edmond's maximum weighted matching algorithm
> ### Aliases: LocalRecProg
> ### Keywords: manip
> 
> ### ** Examples
> 
> # LocalRecProg
> data(testdata2)
> r1=LocalRecProg(testdata2,
+   categorical=c("urbrur", "roof", "walls", "water", "sex", "relat"),
+   missingValue=-99)
> r2=LocalRecProg(testdata2,
+   categorical=c("urbrur", "roof", "walls", "water", "sex", "relat"),
+     ancestor=c("water2", "water3", "relat2"),
+     ancestor_setting=c("water","water","relat"),missingValue=-99)
> r3=LocalRecProg(testdata2,
+   categorical=c("urbrur", "roof", "walls", "water", "sex", "relat"),
+     ancestor=c("water2", "water3", "relat2"),
+     ancestor_setting=c("water","water","relat"),missingValue=-99,
+     FindLowestK=FALSE)
> 
> ## for objects of class sdcMicro:
> data(testdata2)
> sdc <- createSdcObj(testdata2,
+   keyVars=c('urbrur','roof','walls','water','electcon','relat','sex'),
+   numVars=c('expend','income','savings'), w='sampling_weight')
Error in var(if (is.vector(x) || is.factor(x)) x else as.double(x), na.rm = na.rm) : 
  is.atomic(x) is not TRUE
Calls: createSdcObj ... dRiskX -> dRiskWORK -> apply -> FUN -> var -> stopifnot
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘sdcMicro.Rmd’ using rmarkdown
--- finished re-building ‘sdcMicro.Rmd’

--- re-building ‘sdc_guidelines.rnw’ using knitr
Quitting from lines 193-205 (sdc_guidelines.rnw) 
Error: processing vignette 'sdc_guidelines.rnw' failed with diagnostics:
is.atomic(x) is not TRUE
--- failed re-building ‘sdc_guidelines.rnw’

SUMMARY: processing the following file failed:
  ‘sdc_guidelines.rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   3.8Mb
Namespace in Imports field not imported from: 'lpSolveAPI'
  All declared Imports should be used.
Undeclared package ‘RegSDC’ in Rd xrefs
estimateTimeToComputeTargetDefinition: no visible global function
  definition for ‘flush.console’
estimateTimeToComputeTargetDefinition: no visible global function
  definition for ‘combn’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘flush.console’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘combn’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘quantile’
initialize,sdcTargetMatrixClass: no visible global function definition
  for ‘flush.console’
Undefined global functions or variables:
  combn flush.console quantile
Consider adding
  importFrom("stats", "quantile")
  importFrom("utils", "combn", "flush.console")
to your NAMESPACE file.
File ‘SDDE/libs/SDDE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘result.txt’
.ACF.compute: no visible global function definition for ‘pnorm’
.ACF.compute: no visible global function definition for ‘qnorm’
.ACF.compute: no visible global function definition for ‘pchisq’
.ACF.plot: no visible global function definition for ‘abline’
.ADF.compute: no visible global function definition for ‘qnorm’
.ADF.compute: no visible global function definition for ‘chisq.test’
.ADF.compute: no visible global function definition for ‘qchisq’
.ADF.compute: no visible global function definition for ‘pchisq’
.ADF.plot: no visible global function definition for ‘abline’
.CADF.plot: no visible global function definition for ‘points’
.DeltaADF.plot: no visible global function definition for ‘abline’
.RPADF.compute: no visible global function definition for ‘pchisq’
.RPADF.compute: no visible global function definition for ‘qchisq’
.RPADF.plot: no visible global function definition for ‘abline’
.RPADF.plot: no visible global function definition for ‘rect’
.fmin: no visible global function definition for ‘optimize’
.fobj: no visible global function definition for ‘pchisq’
.gen.plot: no visible global function definition for ‘axis’
.gen.plot: no visible global function definition for ‘box’
.gen.plot: no visible global function definition for ‘abline’
.lcv: no visible global function definition for ‘bw.nrd0’
.lcv: no visible global function definition for ‘nlm’
ADF: no visible binding for global variable ‘p.adjust.methods’
ADF: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  abline axis box bw.nrd0 chisq.test nlm optimize p.adjust
  p.adjust.methods pchisq pnorm points qchisq qnorm rect
Consider adding
  importFrom("graphics", "abline", "axis", "box", "points", "rect")
  importFrom("stats", "bw.nrd0", "chisq.test", "nlm", "optimize",
             "p.adjust", "p.adjust.methods", "pchisq", "pnorm", "qchisq",
             "qnorm")
to your NAMESPACE file.
Found the following files/directories:
  ‘MC p-value.ps’ ‘Output.csv’ ‘Rh.ps’ ‘Th.ps’ ‘dataratio .Rdata’
  ‘featuresRmax.csv’ ‘featuresT.csv’
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.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’ ‘tidyr’
  All declared Imports should be used.
dimplot: no visible global function definition for ‘par’
dimplot: no visible global function definition for ‘barplot’
dimplot: no visible global function definition for ‘axis’
find.traj: no visible global function definition for ‘flush.console’
nullprob: no visible global function definition for ‘pbinom’
pbox: no visible global function definition for ‘rect’
pbox: no visible global function definition for ‘par’
prim.traj: no visible global function definition for ‘flush.console’
prim.trajauto: no visible global function definition for
  ‘flush.console’
resampstats: no visible binding for global variable ‘sd’
scatterbox: no visible binding for global variable ‘box’
sd.start: no visible global function definition for ‘read.csv’
sd.start: no visible global function definition for ‘par’
sd.start: no visible global function definition for ‘graphics.off’
sd.start: no visible global function definition for ‘hist’
sd.start: no visible global function definition for ‘plot.ecdf’
sd.start: no visible global function definition for ‘write.csv’
sd.start: no visible global function definition for ‘flush.console’
trajplot: no visible global function definition for ‘points’
trajplot: no visible global function definition for ‘flush.console’
trajplot: no visible global function definition for ‘lm’
trajplot: no visible global function definition for ‘predict.lm’
trajplot: no visible global function definition for ‘identify’
Undefined global functions or variables:
  axis barplot box flush.console graphics.off hist identify lm par
  pbinom plot.ecdf points predict.lm read.csv rect sd write.csv
Consider adding
  importFrom("grDevices", "graphics.off")
  importFrom("graphics", "axis", "barplot", "box", "hist", "identify",
             "par", "points", "rect")
  importFrom("stats", "lm", "pbinom", "plot.ecdf", "predict.lm", "sd")
  importFrom("utils", "flush.console", "read.csv", "write.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘demofile.txt’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Package in Depends field not imported from: ‘lars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
sealasso: no visible global function definition for ‘lars’
weight.calc: no visible global function definition for ‘lars’
Undefined global functions or variables:
  lars
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R   7.1Mb
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.
Rd file 'createTree.Rd':
  \usage lines wider than 90 characters:
     createTree(data, treeType = "quad", dataType = "point", columns = if (dataType=="point") 1:2 else 1:4, ...)

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
adx: no visible global function definition for ‘abline’
adx: no visible global function definition for ‘legend’
dx: no visible global function definition for ‘abline’
dx: no visible global function definition for ‘legend’
maxd: no visible global function definition for ‘abline’
maxd: no visible global function definition for ‘legend’
pc: no visible global function definition for ‘rainbow’
pc: no visible global function definition for ‘abline’
pc: no visible global function definition for ‘legend’
pc: no visible global function definition for ‘points’
pcu: no visible global function definition for ‘rainbow’
pcu: no visible global function definition for ‘abline’
pcu: no visible global function definition for ‘legend’
pcu: no visible global function definition for ‘points’
rmsd: no visible global function definition for ‘abline’
rmsd: no visible global function definition for ‘legend’
rsd: no visible global function definition for ‘abline’
rsd: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline legend points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "points")
to your NAMESPACE file.
Note: found 3 marked UTF-8 strings
Package in Depends field not imported from: ‘JM’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SEchart: no visible global function definition for ‘rect’
SEchart: no visible global function definition for ‘par’
SEchart: no visible global function definition for ‘grid’
SEchart: no visible global function definition for ‘axis’
SEchart: no visible global function definition for ‘text’
SEchart: no visible global function definition for ‘lines’
SEchart: no visible global function definition for ‘heat.colors’
SEchart: no visible global function definition for ‘topo.colors’
SEchart: no visible global function definition for ‘cm.colors’
SEchart: no visible global function definition for ‘terrain.colors’
SEchart: no visible global function definition for ‘gray.colors’
SEchart: no visible global function definition for ‘rainbow’
SEchart: no visible global function definition for ‘points’
SEchart: no visible global function definition for ‘legend’
Undefined global functions or variables:
  axis cm.colors gray.colors grid heat.colors legend lines par points
  rainbow rect terrain.colors text topo.colors
Consider adding
  importFrom("grDevices", "cm.colors", "gray.colors", "heat.colors",
             "rainbow", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "points", "rect", "text")
to your NAMESPACE file.
Undeclared package ‘Hmisc’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
fdc2s: no visible global function definition for ‘lm’
fdc3s: no visible global function definition for ‘lm’
fds2s: no visible global function definition for ‘lm’
fds3s: no visible global function definition for ‘lm’
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  14.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘fansi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rsbml’
Undeclared packages ‘EDNE.EQ’, ‘T2EQ’ in Rd xrefs
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
get.infectiousness: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  qchisq
Consider adding
  importFrom("stats", "qchisq")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘cluster’ ‘factoextra’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘FD’
  All declared Imports should be used.
get_statistics_from_file: no visible global function definition for
  ‘read.csv’
glm_anova: no visible global function definition for ‘aov’
glm_anova: no visible global function definition for ‘glm’
glm_anova: no visible global function definition for ‘gaussian’
glm_anova: no visible global function definition for ‘anova’
glm_anova: no visible global function definition for ‘quasipoisson’
glm_anova: no visible global function definition for ‘sd’
glm_anova: no visible global function definition for ‘p.adjust’
ttest_cohens_d: no visible global function definition for ‘t.test’
ttest_cohens_d: no visible global function definition for ‘sd’
Undefined global functions or variables:
  anova aov gaussian glm p.adjust quasipoisson read.csv sd t.test
Consider adding
  importFrom("stats", "anova", "aov", "gaussian", "glm", "p.adjust",
             "quasipoisson", "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘expression.csv’ ‘group.csv’
'LazyData' is specified without a 'data' directory
predict.SEL: warning in splineDesign(newdata, knots = knts, ord =
  object$nord, deriv = rep(deriv, length(newdata)), outer.ok = TRUE):
  partial argument match of 'deriv' to 'derivs'
getbinPost: no visible binding for global variable ‘dbeta’
getbinPost: no visible binding for global variable ‘pbeta’
getbinPost : fu: no visible global function definition for ‘dbinom’
getbinPost : fu: no visible global function definition for ‘predict’
getbinPost: no visible global function definition for ‘integrate’
getbinPost: no visible global function definition for ‘splinefun’
int.funct: no visible global function definition for ‘integrate’
int.funct2: no visible global function definition for ‘integrate’
min.abs: no visible global function definition for ‘uniroot’
print.SEL: no visible global function definition for ‘integrate’
print.summary.SEL : foo1: no visible global function definition for
  ‘predict’
print.summary.SEL : foo2: no visible global function definition for
  ‘predict’
print.summary.SEL: no visible global function definition for
  ‘integrate’
quantSEL: no visible global function definition for ‘predict’
quantSEL: no visible global function definition for ‘splinefun’
rvSEL: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbeta dbinom integrate pbeta predict runif splinefun uniroot
Consider adding
  importFrom("stats", "dbeta", "dbinom", "integrate", "pbeta", "predict",
             "runif", "splinefun", "uniroot")
to your NAMESPACE file.
File ‘SEL/libs/SEL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: ‘sem’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'semdiag.Rd':
  \usage lines wider than 90 characters:
     semdiag(x,  EQSmodel, varphi=0.1, EQSdata='data.txt', D='E', delete=integer(0), max_it=1000, EQSprog='C:/Progra~1/EQS61/WINEQS',serial= ... [TRUNCATED]

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

These lines will be truncated in the PDF manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lavaan’ ‘psych’ ‘semPlot’ ‘semTools’ ‘shinyAce’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ROntoTools’
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘webp’
  All declared Imports should be used.
Running ‘testthat.R’ [62s/266s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(seminr)
  > Sys.unsetenv("R_TESTS")
  > test_check("seminr")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • empty test (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-bootstrap.R:329:3): Seminr calculates descriptives correctly with missing values ──
  descriptives[, 8] not equal to boot_item_control[, 8].
  50/50 mismatches (average diff: 0.433)
  [1] 2.62 - 2.48 ==  0.1409
  [2] 2.62 - 1.32 ==  1.2950
  [3] 2.62 - 2.60 ==  0.0130
  [4] 2.62 - 2.43 ==  0.1908
  [5] 2.62 - 2.52 ==  0.0965
  [6] 2.62 - 2.53 ==  0.0911
  [7] 2.62 - 2.30 ==  0.3208
  [8] 2.62 - 2.36 ==  0.2553
  [9] 2.62 - 2.91 == -0.2881
  ...
  ── Failure (test-bootstrap.R:330:3): Seminr calculates descriptives correctly with missing values ──
  descriptives[, 9] not equal to boot_item_control[, 9].
  50/50 mismatches (average diff: 0.519)
  [1] 0.0843 -  0.7435 == -0.659
  [2] 0.0843 - -0.5681 ==  0.652
  [3] 0.0843 - -0.0418 ==  0.126
  [4] 0.0843 -  0.4953 == -0.411
  [5] 0.0843 - -0.0610 ==  0.145
  [6] 0.0843 -  0.1957 == -0.111
  [7] 0.0843 - -0.0417 ==  0.126
  [8] 0.0843 - -0.1411 ==  0.225
  [9] 0.0843 - -0.5648 ==  0.649
  ...
  ── Failure (test-descriptive-stats.R:46:3): Seminr estimates the item descriptives correctly ──
  item_stats[1:24, 1:9] not equal to item_stats_control[1:24, 1:9].
  48/216 mismatches (average diff: 0.382)
  [169] 3.88 - 3.86 ==  0.0246
  [170] 3.88 - 4.48 == -0.5985
  [171] 3.88 - 3.64 ==  0.2399
  [172] 3.88 - 3.18 ==  0.7062
  [173] 3.88 - 3.59 ==  0.2978
  [174] 3.88 - 3.99 == -0.1090
  [175] 3.88 - 3.26 ==  0.6199
  [176] 3.88 - 3.10 ==  0.7828
  [177] 3.88 - 2.11 ==  1.7739
  ...
  
  [ FAIL 3 | WARN 0 | SKIP 3 | PASS 195 ]
  Error: Test failures
  Execution halted
Malformed Description field: should contain one or more complete sentences.
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.
ChiSquaredLRTest: no visible global function definition for ‘na.omit’
ChiSquaredLRTest: no visible global function definition for ‘cov’
ChiSquaredLRTest: no visible global function definition for ‘dmvnorm’
ChiSquaredLRTest: no visible global function definition for ‘pchisq’
NormalTheoryLRTest: no visible global function definition for ‘na.omit’
NormalTheoryLRTest: no visible global function definition for ‘cov’
NormalTheoryLRTest: no visible global function definition for ‘dmvnorm’
NormalTheoryLRTest: no visible global function definition for ‘sd’
NormalTheoryLRTest: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  cov dmvnorm na.omit pchisq pnorm sd
Consider adding
  importFrom("stats", "cov", "na.omit", "pchisq", "pnorm", "sd")
to your NAMESPACE file.
Running examples in ‘SEMModComp-Ex.R’ failed
The error most likely occurred in:

> ### Name: ChiSquaredLRTest
> ### Title: Conduct Chi-Squared Likelihood Ratio Test for Mean and
> ###   Covariance Structure Models
> ### Aliases: ChiSquaredLRTest
> ### Keywords: htest multivariate
> 
> ### ** Examples
> 
>   # Load the data, model-implied moments, and degrees of freedom for the
>   # comparison of Model A to Model C (the BFPD-C) in Levy and Hancock (2007)
>   data(cigandalc.dat)
>   data(model.A.mean.vector)
>   data(model.A.cov.matrix)
>   data(model.A.df)
>   data(model.C.mean.vector)
>   data(model.C.cov.matrix)
>   data(model.C.df)
>   
>   # Conduct the chi-squared difference LR test for the comparison of Model A 
>   # to Model C (the BFPD-C) in Levy and Hancock (2007)
>   LR.model.A.to.model.C  <- ChiSquaredLRTest(
+ 	x = cigandalc.dat,
+ 	model.1.mean.vector = model.C.mean.vector,
+ 	model.1.cov.matrix = model.C.cov.matrix,
+ 	model.1.df = model.C.df,
+ 	model.2.mean.vector = model.A.mean.vector,
+ 	model.2.cov.matrix = model.A.cov.matrix,
+ 	model.2.df = model.A.df
+   )

CHI-SQUARED LR TEST OUTPUT

Error in t(x) - mean : non-numeric argument to binary operator
Calls: ChiSquaredLRTest -> dmvnorm -> backsolve
Execution halted
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘editData’ ‘miniUI’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Undeclared package ‘SemNetCleaner’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grid’ ‘purrr’
  All declared Imports should be used.
Undeclared packages ‘NetworkToolbox’, ‘SemNetCleaner’ in Rd xrefs
'library' or 'require' calls in package code:
  ‘XML’ ‘boot’ ‘sem’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  ‘boot:::const’ ‘stats:::AIC.logLik’ ‘stats:::BIC.logLik’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘addPath.plsm’ ‘endogenous’ ‘predecessors’ ‘qSquared’ ‘reorder’
  ‘resempls’ ‘residuals.sempls’
Undeclared package ‘qgraph’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
.plot_attachment: no visible global function definition for ‘dev.off’
.update_list: no visible global function definition for ‘modifyList’
mime_part.data.frame: no visible global function definition for
  ‘write.table’
mime_part.ggplot: no visible binding for global variable ‘pdf’
mime_part.matrix: no visible global function definition for
  ‘write.table’
mime_part.trellis: no visible binding for global variable ‘pdf’
Undefined global functions or variables:
  dev.off modifyList pdf write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "modifyList", "write.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘informal_benchmarking.Rmd’ using rmarkdown
--- finished re-building ‘informal_benchmarking.Rmd’

--- re-building ‘sensemakr.Rmd’ using rmarkdown
Quitting from lines 68-69 (sensemakr.Rmd) 
Error: processing vignette 'sensemakr.Rmd' failed with diagnostics:
cannot coerce class '"lm"' to a data.frame
--- failed re-building ‘sensemakr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
gconv: no visible global function definition for ‘convolve’
sens.analysis.aberrant.rank: no visible global function definition for
  ‘pnorm’
sens.analysis.mh: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  convolve pnorm
Consider adding
  importFrom("stats", "convolve", "pnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
mscorev: no visible global function definition for ‘quantile’
senmwCI : funcCI: no visible global function definition for ‘qnorm’
senmwCI : funcCI2: no visible global function definition for ‘qnorm’
separable1k: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm quantile
Consider adding
  importFrom("stats", "pnorm", "qnorm", "quantile")
to your NAMESPACE file.
plot.sensitivity.2.0d: no visible global function definition for ‘gray’
sensitivitySGD: no visible global function definition for ‘tail’
sensitivitySGL: no visible global function definition for ‘tail’
Undefined global functions or variables:
  gray tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("utils", "tail")
to your NAMESPACE file.
File ‘sensitivityPStrat/libs/sensitivityPStrat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    libs   2.6Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs    15.0Mb
    models   1.3Mb
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.0Mb
Note: found 4436 marked UTF-8 strings
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘assocpointpair_result.csv’ ‘foundereffectfinder_result.csv’
  ‘getfreqs_result.csv’ ‘getfreqs_result.png’ ‘orPlot.pdf1_1.pdf’
  ‘orPlot.pdf2_1.pdf’ ‘orPlot.pdf3_1.pdf’ ‘orPlot.pdf4_1.pdf’
  ‘orPlot.pdf5_1.pdf’ ‘orPlot.pdf6_1.pdf’ ‘orPlot.pdf7_1.pdf’
  ‘orPlot.pdf8_1.pdf’ ‘q-values_result.csv’ ‘rewritetuple_result.csv’
  ‘tartan_plot.pdf’ ‘vispair_plot.pdf’ ‘vispairfeat_plot.pdf’
  ‘volcano_plot.pdf’
'LazyData' is specified without a 'data' directory
Running examples in ‘seqhandbook-Ex.R’ failed
The error most likely occurred in:

> ### Name: seq_heatmap
> ### Title: Index plot of sequences ordered according to a dendrogram
> ### Aliases: seq_heatmap
> 
> ### ** Examples
> 
> if (require(TraMineR)) {
+   data(mvad)
+   mvad.seq <- seqdef(mvad[,17:86])
+   mvad.lcs <- seqdist(mvad.seq, method = "LCS")
+   mvad.hc <- hclust(as.dist(mvad.lcs), method = "ward.D2")
+   seq_heatmap(mvad.seq, mvad.hc)
+ }
 [>] 6 distinct states appear in the data: 
     1 = FE
     2 = HE
     3 = employment
     4 = joblessness
     5 = school
     6 = training
 [>] state coding:
       [alphabet]  [label]     [long label] 
     1  FE          FE          FE
     2  HE          HE          HE
     3  employment  employment  employment
     4  joblessness joblessness joblessness
     5  school      school      school
     6  training    training    training
 [>] 712 sequences in the data set
 [>] min/max sequence length: 70/70
Error in dimnames(x) <- dn : 
  length of 'dimnames' [1] not equal to array extent
Calls: seqdist -> seqdur -> seqasnum -> rownames<-
Execution halted
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    libs  12.4Mb
Running examples in ‘seqHMM-Ex.R’ failed
The error most likely occurred in:

> ### Name: simulate_hmm
> ### Title: Simulate hidden Markov models
> ### Aliases: simulate_hmm
> 
> ### ** Examples
> 
> # Parameters for the HMM
> emission_probs <- matrix(c(0.5, 0.2, 0.5, 0.8), 2, 2)
> transition_probs <- matrix(c(5/6, 1/6, 1/6, 5/6), 2, 2)
> initial_probs <- c(1, 0)
> 
> # Setting the seed for simulation
> set.seed(1)
> 
> # Simulating sequences
> sim <- simulate_hmm(
+   n_sequences = 10, initial_probs = initial_probs, 
+   transition_probs = transition_probs, 
+   emission_probs = emission_probs, 
+   sequence_length = 20)
>   
> ssplot(sim, sortv = "mds.obs", type = "I")
Error in dimnames(x) <- dn : 
  length of 'dimnames' [1] not equal to array extent
Calls: ssplot -> do.call -> <Anonymous>
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
plotenz : addmark: no visible global function definition for ‘par’
plotenz : addmark: no visible global function definition for ‘text’
plotenz : addmark: no visible global function definition for ‘segments’
plotenz : addband: no visible global function definition for ‘segments’
plotenz : addband: no visible global function definition for ‘text’
plotenz: no visible global function definition for ‘layout’
plotenz: no visible global function definition for ‘text’
plotenz: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  dev.new layout par segments text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "layout", "par", "segments", "text")
to your NAMESPACE file.
Rd file 'plotenz.Rd':
  \usage lines wider than 90 characters:
     plotenz(sequences, enznames, enzdata, side = TRUE, type = c("RFLP", "TRFLP"), Terminal = c("T5", "T3"))

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘total’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
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.
'LazyData' is specified without a 'data' directory
Running examples in ‘seriation-Ex.R’ failed
The error most likely occurred in:

> ### Name: Psych24
> ### Title: Results of 24 Psychological Test for 8th Grade Students
> ### Aliases: Psych24
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data("Psych24")
> 
> ## create a dist object and also get rid of the one negative entry in the
> ## correlation matrix
> d <- as.dist(1 - abs(Psych24))
> 
> pimage(d)
> 
> ## do hclust as in Ling (1973)
> hc <- hclust(d, method = "complete")
> plot(hc)
> 
> pimage(d, hc)
Error in ser_permutation_vector(obj) : 
  'list' object cannot be coerced to type 'integer'
Calls: pimage ... ser_permutation -> lapply -> FUN -> ser_permutation_vector
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > 
  > library("seriation")
  > test_check("seriation")
  Doing  ARSA  ... took  0.004 s.
  Doing  BBURCG  ... took  0.005 s.
  Doing  BBWRCG  ... took  0.004 s.
  Doing  GW  ... ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-permuation_vector.R:26:1): (code run outside of `test_that()`) ──
  Error in `ser_permutation_vector(obj)`: 'list' object cannot be coerced to type 'integer'
  Backtrace:
      █
   1. ├─testthat::expect_identical(length(ser_permutation(sp, hc)), 2L) test-permuation_vector.R:26:0
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─seriation::ser_permutation(sp, hc)
   5.   └─base::lapply(...)
   6.     └─seriation:::FUN(X[[i]], ...)
   7.       └─seriation::ser_permutation_vector(obj)
  ── Error (test-seriate.R:17:1): (code run outside of `test_that()`) ────────────
  Error in `ser_permutation_vector(order, method = method$name)`: 'list' object cannot be coerced to type 'integer'
  Backtrace:
      █
   1. └─base::sapply(...) test-seriate.R:17:0
   2.   └─base::lapply(X = X, FUN = FUN, ...)
   3.     └─seriation:::FUN(X[[i]], ...)
   4.       ├─base::system.time(o <- seriate(d, method = m)) test-seriate.R:19:2
   5.       ├─seriation::seriate(d, method = m)
   6.       └─seriation:::seriate.dist(d, method = m)
   7.         ├─seriation::ser_permutation(ser_permutation_vector(order, method = method$name))
   8.         └─seriation::ser_permutation_vector(order, method = method$name)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 64 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘seriation.Rnw’ using Sweave

Error: processing vignette 'seriation.Rnw' failed with diagnostics:
 chunk 11 
Error in ser_permutation_vector(order, method = method$name) : 
  'list' object cannot be coerced to type 'integer'

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
Malformed Title field: should not end in a period.
capture: no visible binding for global variable ‘resultText’
restore.session: no visible binding for global variable
  ‘.save.session.packages’
restore.session: no visible binding for global variable
  ‘.save.session.search’
save.session: no visible global function definition for ‘dev.list’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.search’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.packages’
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.
Found the following files/directories:
  ‘RSession.Rda’
Running examples in ‘SetMethods-Ex.R’ failed
The error most likely occurred in:

> ### Name: LR.intersect
> ### Title: Function for identifying contradictory simplifying assumptions
> ###   or easy counterfactuals.
> ### Aliases: LR.intersect
> ### Keywords: QCA
> 
> ### ** Examples
> 
> # Import your data. For example:
> 
> data(SCHF)
> 
> # Get the parsimonious solution:
> 
> sol_yp <- minimize(SCHF, outcome = "EXPORT",
+                 conditions = c("EMP","BARGAIN","UNI","OCCUP","STOCK", "MA"),
+                 incl.cut = .9, 
+                 include = "?", 					   
+                 details = TRUE, show.cases = TRUE)

Error: Input vectors should be numeric or logical.

Execution halted
setpath: no visible global function definition for ‘cov’
setpath: no visible global function definition for ‘median’
setpath: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cov median pchisq
Consider adding
  importFrom("stats", "cov", "median", "pchisq")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
random.number.test: no visible global function definition for ‘runif’
random.number.test: no visible global function definition for ‘rnorm’
setRNG: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘plotly’ in Rd xrefs
Imports includes 41 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   7.0Mb
Undeclared package ‘Signac’ in Rd xrefs
'library' or 'require' call to ‘graphics’ which was already attached by Depends.
  Please remove these calls from your code.
severity: no visible global function definition for ‘qnorm’
severity: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
L_exp: no visible global function definition for ‘pnorm’
L_hNV: no visible global function definition for ‘pnorm’
L_trunc: no visible global function definition for ‘pnorm’
L_trunc_mufest: no visible global function definition for ‘pnorm’
dgp: no visible global function definition for ‘runif’
dgp: no visible global function definition for ‘rnorm’
eff.sfa: no visible global function definition for ‘predict’
fitted.sfa: no visible global function definition for ‘predict’
predict.sfa: no visible global function definition for ‘coef’
print.sfa: no visible global function definition for ‘coef’
residuals.sfa: no visible global function definition for ‘fitted’
sfa: no visible global function definition for ‘model.frame’
sfa: no visible global function definition for ‘model.response’
sfa.fit: no visible global function definition for ‘lm’
sfa.fit: no visible global function definition for ‘resid’
sfa.fit: no visible global function definition for ‘var’
sfa.fit: no visible global function definition for ‘optim’
summary.sfa: no visible global function definition for ‘logLik’
summary.sfa: no visible global function definition for ‘pchisq’
te.eff.sfa: no visible global function definition for ‘residuals’
te.eff.sfa: no visible global function definition for ‘pnorm’
u.sfa: no visible global function definition for ‘residuals’
u.sfa: no visible global function definition for ‘dnorm’
u.sfa: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  coef dnorm fitted lm logLik model.frame model.response optim pchisq
  pnorm predict resid residuals rnorm runif var
Consider adding
  importFrom("stats", "coef", "dnorm", "fitted", "lm", "logLik",
             "model.frame", "model.response", "optim", "pchisq", "pnorm",
             "predict", "resid", "residuals", "rnorm", "runif", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
Namespace in Imports field not imported from: ‘geometries’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    doc      1.7Mb
    libs     8.2Mb
    sqlite   1.5Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘tripack’ in Rd xrefs
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 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Malformed Description field: should contain one or more complete sentences.
.computePStar: no visible global function definition for ‘uniroot’
plotBoundary: no visible global function definition for
  ‘scale_y_continuous’
Undefined global functions or variables:
  scale_y_continuous uniroot
Consider adding
  importFrom("stats", "uniroot")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘sGMRFmix-Ex.R’ failed
The error most likely occurred in:

> ### Name: compute_anomaly_score
> ### Title: Compute anomaly scores
> ### Aliases: compute_anomaly_score
> 
> ### ** Examples
> 
> library(sGMRFmix)
> 
> set.seed(314)
> train_data <- generate_train_data()
> fit <- sGMRFmix(train_data, K = 7, rho = 10)
################## sparseGaussMix #######################

  |                                                                            
  |                                                                      |   0%Error in t(x) - mean : non-numeric argument to binary operator
Calls: sGMRFmix ... sparseGaussMix -> lapply -> FUN -> dmvnorm -> backsolve
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sGMRFmix)
  > 
  > test_check("sGMRFmix")
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |                                                                      |   0%══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-sGMRFmix.R:6:3): main function ──────────────────────────────────
  Error in `t(x) - mean`: non-numeric argument to binary operator
  Backtrace:
      █
   1. └─sGMRFmix::sGMRFmix(x, K = 7, rho = 100) test-sGMRFmix.R:6:2
   2.   └─sGMRFmix:::sparseGaussMix(...)
   3.     └─base::lapply(...)
   4.       └─sGMRFmix:::FUN(X[[i]], ...)
   5.         └─mvtnorm::dmvnorm(x, mean = m[[k]], sigma = invLambda[[k]], log = TRUE)
   6.           └─base::backsolve(dec, t(x) - mean, transpose = TRUE)
  ── Error (test-sGMRFmix.R:15:3): compute anomaly ───────────────────────────────
  Error in `t(x) - mean`: non-numeric argument to binary operator
  Backtrace:
      █
   1. └─sGMRFmix::sGMRFmix(x, K = 7, rho = 100) test-sGMRFmix.R:15:2
   2.   └─sGMRFmix:::sparseGaussMix(...)
   3.     └─base::lapply(...)
   4.       └─sGMRFmix:::FUN(X[[i]], ...)
   5.         └─mvtnorm::dmvnorm(x, mean = m[[k]], sigma = invLambda[[k]], log = TRUE)
   6.           └─base::backsolve(dec, t(x) - mean, transpose = TRUE)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘sGMRFmix.Rmd’ using rmarkdown
Quitting from lines 57-60 (sGMRFmix.Rmd) 
Error: processing vignette 'sGMRFmix.Rmd' failed with diagnostics:
non-numeric argument to binary operator
--- failed re-building ‘sGMRFmix.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.4Mb
amse: no visible global function definition for ‘na.omit’
arb: no visible global function definition for ‘na.omit’
rdatagen: no visible global function definition for ‘qnorm’
rdatagen: no visible global function definition for ‘pbinom’
rdatagen: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  na.omit pbinom pnorm qnorm
Consider adding
  importFrom("stats", "na.omit", "pbinom", "pnorm", "qnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘foreign’ which was already attached by Depends.
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyDataCompression' is specified without 'LazyData'
Namespaces in Imports field not imported from:
  ‘MASS’ ‘kableExtra’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hydromad’
Running examples in ‘shattering-Ex.R’ failed
The error most likely occurred in:

> ### Name: estimate_number_hyperplanes
> ### Title: Function to estimate the number of hyperplanes required to
> ###   classify such a data sample.
> ### Aliases: estimate_number_hyperplanes
> ### Keywords: estimate hyperplanes number
> 
> ### ** Examples
> 
> 
> # Generating some random dataset with 2 classes:
> # 50 examples in class 1 and 50 in class 2 (last column)
> data = cbind(rnorm(mean=1, sd=1, n=50), rnorm(mean=1, sd=1, n=50), rep(1, 50))
> data = rbind(data, cbind(rnorm(mean=-1, sd=1, n=50), rnorm(mean=-1, sd=1, n=50), rep(2, 50)))
> 
> # Building up the input and output sets
> X = data[,1:2]
> Y = data[,3]
> 
> # Plotting our dataset using classes as colors
> plot(X, col=Y, main="Original dataset", xlab="Attribute 1", ylab="Attribute 2")
> 
> # Here we estimate the number of hyperplanes required to shatter (divide) the given sample
> # in all possible ways according to the organization of points in the input space
> Hyperplanes = estimate_number_hyperplanes(X, Y, length=10, quantile.percentage=0.1, epsilon=1e-7)
Error in structure(.Internal(as.vector(x, "double")), Csingle = TRUE) : 
  'list' object cannot be coerced to type 'double'
Calls: estimate_number_hyperplanes ... <Anonymous> -> as.single -> as.single.default -> structure
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(shattering)
  > 
  > test_check("shattering")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test01.r:4:1): (code run outside of `test_that()`) ───────────────────
  Error in `structure(.Internal(as.vector(x, "double")), Csingle = TRUE)`: 'list' object cannot be coerced to type 'double'
  Backtrace:
      █
   1. └─shattering::estimate_number_hyperplanes(...) test01.r:4:0
   2.   └─shattering::equivalence_relation(...)
   3.     ├─base::matrix(...)
   4.     └─pdist::pdist(X, indices.A = ids[elements], indices.B = 1:nrow(X))
   5.       ├─base::as.single(as.vector(Y))
   6.       └─base::as.single.default(as.vector(Y))
   7.         └─base::structure(.Internal(as.vector(x, "double")), Csingle = TRUE)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
popify: no visible global function definition for ‘runif’
tipify: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    www   9.4Mb
'LazyData' is specified without a 'data' directory
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    www  16.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reactable’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘CTT’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘scales’ ‘websocket’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘finetune’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    shinyApp  21.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘shiny’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    www   7.2Mb
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    help   2.5Mb
    www    8.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.shiny_run’ ‘shinyShortcut.desktop’
'LazyData' is specified without a 'data' directory
Undeclared package ‘brms’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
shrink.estim: no visible global function definition for ‘cov’
shrink.estim: no visible global function definition for ‘cor’
shrink.estim: no visible global function definition for ‘cov2cor’
targetCor: no visible global function definition for ‘cor.test’
targetCor: no visible global function definition for ‘cor’
targetCor: no visible global function definition for ‘sd’
targetCor: no visible global function definition for ‘cov’
targetD: no visible binding for global variable ‘var’
targetF: no visible global function definition for ‘cov’
targetF: no visible global function definition for ‘cor’
targetG: no visible global function definition for ‘cor’
targetG: no visible global function definition for ‘sd’
targetG: no visible global function definition for ‘cov’
targetGpos: no visible global function definition for ‘cor’
targetGpos: no visible global function definition for ‘sd’
targetGpos: no visible global function definition for ‘cov’
targetGstar: no visible global function definition for ‘cor’
targetGstar: no visible global function definition for ‘sd’
targetGstar: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cor cor.test cov cov2cor sd var
Consider adding
  importFrom("stats", "cor", "cor.test", "cov", "cov2cor", "sd", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Requires orphaned package: ‘mfp’
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Depends: includes the non-default packages:
  'hdrcde', 'coda', 'MASS', 'bayesm', 'mnormt', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘MASS’ ‘bayesm’ ‘coda’ ‘hdrcde’ ‘mnormt’ ‘spatstat’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'siarmcmcdirichletv4.Rd':
  \usage lines wider than 90 characters:
     siarmcmcdirichletv4(data, sources, corrections = 0, concdep = 0, iterations=200000, burnin=50000, howmany=10000, thinby=15, prior = rep ... [TRUNCATED]

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 2397 marked UTF-8 strings
Packages in Depends field not imported from:
  ‘ade4’ ‘corpcor’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
filter.PCA.default: no visible global function definition for
  ‘princomp’
filter.mRMR.default: no visible global function definition for
  ‘discretize’
gaussian.default: no visible global function definition for ‘cov’
gaussian.default: no visible global function definition for
  ‘cov.shrink’
plot.verify.cv: no visible global function definition for ‘points’
plot.verify.ho: no visible global function definition for ‘points’
plot.verify.loo: no visible global function definition for ‘points’
predict.dpa1: no visible global function definition for ‘cor’
predict.filter.PCA: no visible global function definition for ‘predict’
predict.filter.RegressionTreeFilter: no visible global function
  definition for ‘is.struct’
predict.filter.RegressionTreeFilter: no visible global function
  definition for ‘var’
simulator.Simple1: no visible global function definition for ‘rnorm’
verify.ho.default: no visible global function definition for ‘predict’
verify.loo.default: no visible global function definition for ‘predict’
Undefined global functions or variables:
  cor cov cov.shrink discretize is.struct points predict princomp rnorm
  var
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "cor", "cov", "predict", "princomp", "rnorm",
             "var")
to your NAMESPACE file.
Rd file 'plot.verify.ho.Rd':
  \examples lines wider than 100 characters:
     attack=verify.ho(model=gaussian,filter=filter.PCA,Xlearn=traces[1:128,],Ylearn=key[1:128],Xval=traces[129:256,],Yval=key[129:256],nbreV ... [TRUNCATED]

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

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

These lines will be truncated in the PDF manual.
dSepAdji: no visible global function definition for ‘as’
dag2cpdagAdj: no visible global function definition for ‘as’
randomDAG: no visible global function definition for ‘rbinom’
structIntervDist: no visible global function definition for ‘as’
Undefined global functions or variables:
  as rbinom
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "rbinom")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘sievePH-Ex.R’ failed
The error most likely occurred in:

> ### Name: testDensRatioGOF
> ### Title: Goodness-of-Fit Test of the Validity of a Univariate or
> ###   Multivariate Mark Density Ratio Model
> ### Aliases: testDensRatioGOF
> 
> ### ** Examples
> 
> n <- 500
> tx <- rep(0:1, each=n/2)
> tm <- c(rexp(n/2, 0.2), rexp(n/2, 0.2 * exp(-0.4)))
> cens <- runif(n, 0, 15)
> eventTime <- pmin(tm, cens, 3)
> eventInd <- as.numeric(tm <= pmin(cens, 3))
> mark1 <- ifelse(eventInd==1, c(rbeta(n/2, 2, 5), rbeta(n/2, 2, 2)), NA)
> mark2 <- ifelse(eventInd==1, c(rbeta(n/2, 1, 3), rbeta(n/2, 5, 1)), NA)
> 
> # test goodness-of-fit for a univariate mark
> testDensRatioGOF(eventInd, mark1, tx, iter=20)
$teststat
[1] 0.7020808

$pval
[1] 0

$DRcoef
    alpha     beta1 
-1.993395  5.255884 

$DRlambda
   lambda 
0.4593023 

> 
> # test goodness-of-fit for a bivariate mark
> testDensRatioGOF(eventInd, data.frame(mark1, mark2), tx, iter=20)
Error in `[.data.frame`(mark, eventInd == 1) : undefined columns selected
Calls: testDensRatioGOF -> [ -> [.data.frame
Execution halted
Found the following files/directories:
  ‘MM.csv’ ‘Simul.csv’ ‘catalytic.csv’
Note: found 1231 marked UTF-8 strings
.cluster: no visible global function definition for ‘kmeans’
.plot.sigclust: no visible global function definition for ‘par’
.plot.sigclust: no visible global function definition for ‘density’
.plot.sigclust: no visible global function definition for ‘runif’
.plot.sigclust: no visible global function definition for ‘dnorm’
.plot.sigclust: no visible global function definition for ‘lines’
.plot.sigclust: no visible global function definition for ‘points’
.plot.sigclust: no visible global function definition for ‘title’
.plot.sigclust: no visible global function definition for ‘text’
.plot.sigclust: no visible global function definition for ‘qnorm’
.plot.sigclust: no visible global function definition for ‘abline’
.plot.sigclust: no visible global function definition for ‘quantile’
.plot.sigclust: no visible global function definition for ‘legend’
.simnull: no visible global function definition for ‘rnorm’
.vareigen: no visible global function definition for ‘mad’
.vareigen: no visible global function definition for ‘cov’
sigclust: no visible global function definition for ‘sd’
sigclust: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline cov density dnorm kmeans legend lines mad par pnorm points
  qnorm quantile rnorm runif sd text title
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "points",
             "text", "title")
  importFrom("stats", "cov", "density", "dnorm", "kmeans", "mad",
             "pnorm", "qnorm", "quantile", "rnorm", "runif", "sd")
to your NAMESPACE file.
Note: found 28 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Imports includes 28 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
File ‘signal/libs/signal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
signmedian.test: no visible global function definition for ‘median’
signmedian.test: no visible global function definition for ‘binom.test’
signmedian.test: no visible global function definition for ‘pbinom’
signmedian.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  binom.test median pbinom pnorm
Consider adding
  importFrom("stats", "binom.test", "median", "pbinom", "pnorm")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘MASS’ ‘class’ ‘cluster’ ‘lattice’ ‘nnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘ExportFigtree1.tre’
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
'library' or 'require' calls in package code:
  ‘gdata’ ‘splines’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.SII: no visible global function definition for ‘lines’
plot.SII: no visible global function definition for ‘abline’
plot.SII: no visible global function definition for ‘legend’
sii : approx.l: no visible global function definition for ‘approx’
sii.excel: no visible global function definition for ‘predict’
sii.excel : approx.l: no visible global function definition for
  ‘approx’
Undefined global functions or variables:
  abline approx legend lines predict
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘car’ ‘ggplot2’ ‘magrittr’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grid’
  All declared Imports should be used.
Undeclared packages ‘GenOrd’, ‘PoisNor’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Error(s) in re-building vignettes:
--- re-building ‘a-simecol-introduction.Rnw’ using Sweave
Loading required package: deSolve
--- finished re-building ‘a-simecol-introduction.Rnw’

--- re-building ‘b-simecol-howtos.Rnw’ using Sweave
Loading required package: FME
Loading required package: rootSolve
Loading required package: coda

Error: processing vignette 'b-simecol-howtos.Rnw' failed with diagnostics:
 chunk 42 
Error in xy.coords(x, y, setLab = FALSE) : 
  'list' object cannot be coerced to type 'double'

--- failed re-building ‘b-simecol-howtos.Rnw’

SUMMARY: processing the following file failed:
  ‘b-simecol-howtos.Rnw’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘digest’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘database.csv’ ‘output.csv’ ‘output_clst.csv’
Namespaces in Imports field not imported from:
  ‘future’ ‘magrittr’ ‘purrr’ ‘rlang’ ‘utils’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Error(s) in re-building vignettes:
--- re-building ‘barrier.Rmd’ using rmarkdown
Quitting from lines 40-75 (barrier.Rmd) 
Error: processing vignette 'barrier.Rmd' failed with diagnostics:
non-conformable arguments
--- failed re-building ‘barrier.Rmd’

--- re-building ‘landscape.Rmd’ using rmarkdown
Quitting from lines 73-78 (landscape.Rmd) 
Error: processing vignette 'landscape.Rmd' failed with diagnostics:
non-conformable arguments
--- failed re-building ‘landscape.Rmd’

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

SUMMARY: processing the following files failed:
  ‘barrier.Rmd’ ‘landscape.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  10.1Mb
Found the following files/directories:
  ‘res_mutation.tsv’ ‘res_mutationCounts.txt’
  ‘res_processContribution.txt’ ‘res_processes.txt’
cumallcausehr: no visible global function definition for ‘integrate’
plotbe: no visible global function definition for ‘lines’
plotbe: no visible global function definition for ‘legend’
plotcph: no visible global function definition for ‘confint’
plotcph: no visible global function definition for ‘abline’
plotcph: no visible global function definition for ‘axis’
plotcph: no visible global function definition for ‘polygon’
plotcph: no visible global function definition for ‘lines’
simCR: no visible global function definition for ‘rnorm’
simEBMT: no visible global function definition for ‘model.matrix’
simexit: no visible global function definition for ‘runif’
simexitinner: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  abline axis confint integrate legend lines model.matrix polygon rnorm
  runif uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "polygon")
  importFrom("stats", "confint", "integrate", "model.matrix", "rnorm",
             "runif", "uniroot")
to your NAMESPACE file.
Undeclared packages ‘BinNonNor’, ‘PoisNor’, ‘PoisBinOrdNor’, ‘PoisBinOrdNonNor’ in Rd xrefs
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Package suggested but not available for checking: ‘clipper’
Found the following files/directories:
  ‘simu.pheno’ ‘usedpars.txt’
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘HISTORY’
File ‘simplexreg/libs/simplexreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
'LazyData' is specified without a 'data' directory
Non-standard file/directory found at top level:
  ‘COPYRIGHTS’
Copyright information should be in file inst/COPYRIGHTS
Package in Depends field not imported from: ‘mclust’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Simpsons: no visible global function definition for ‘Mclust’
Simpsons: no visible global function definition for ‘lm’
Simpsons: no visible global function definition for ‘abline’
Simpsons: no visible global function definition for ‘par’
Simpsons: no visible global function definition for ‘legend’
Simpsons: no visible global function definition for ‘txtProgressBar’
Simpsons: no visible global function definition for ‘setTxtProgressBar’
Simpsons: no visible global function definition for ‘quantile’
plot.Simpson: no visible global function definition for ‘lm’
plot.Simpson: no visible global function definition for ‘abline’
plot.Simpson: no visible global function definition for ‘par’
plot.Simpson: no visible global function definition for ‘legend’
Undefined global functions or variables:
  Mclust abline legend lm par quantile setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "abline", "legend", "par")
  importFrom("stats", "lm", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Found the following files/directories:
  ‘SimRAD-exampleRefSeq-Fasta.fa’ ‘SimRAD-exampleRefSeq.fa’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Found the following files/directories:
  ‘crop_device.pdf’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rgeos’ ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  18.3Mb
Running examples in ‘simukde-Ex.R’ failed
The error most likely occurred in:

> ### Name: simulate_kde
> ### Title: Simulation with Kernel Density Estimation
> ### Aliases: simulate_kde
> 
> ### ** Examples
> 
> ## 1-dimensional data
> data(faithful)
> hist(faithful$eruptions)
> res <- simukde::simulate_kde(x = faithful$eruptions, n = 100, parallel = FALSE)
> hist(res$random.values)
> 
> ## Simulation with the best fitting instrumental distribution
> data(faithful)
> par(mfrow = c(1, 3))
> hist(faithful$eruptions)
> fit <- simukde::find_best_fit(x = faithful$eruptions, positive = TRUE)
> res <- simukde::simulate_kde(
+   x = faithful$eruptions, n = 100,
+   distr = fit$distribution, parallel = FALSE
+ )
> hist(res$random.values)
> par(mfrow = c(1, 1))
> ## Don't show: 
> ## 2-dimensional data
> data(faithful)
> res <- simukde::simulate_kde(x = faithful, n = 1, parallel = FALSE)
Error in linbin(x, gpoints, truncate) : 
  'list' object cannot be coerced to type 'double'
Calls: <Anonymous> -> <Anonymous> -> hpi -> dpik -> linbin
Execution halted
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘crqa’ ‘plot3D’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [86s/112s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(singcar)
  > 
  > test_check("singcar")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-BSDT_cov.R:25:3): input of control_covar can be both dataframe and matrix ──
  Error in `BSDT_cov(case_task = unlist(size_weight_illusion[1, c("V_SWI", 
      "K_SWI")]), case_covar = unlist(size_weight_illusion[1, c("YRS", 
      "MF01")]), control_task = size_weight_illusion[-1, c("V_SWI", 
      "K_SWI")], control_covar = size_weight_illusion[-1, c("YRS", 
      "MF01")], iter = 100)`: Must supply equal number of observations for tasks and covariates
  Backtrace:
      █
   1. └─singcar::BSDT_cov(...) test-BSDT_cov.R:25:2
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 222 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘pracma’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
plotBGpvalues: no visible global function definition for ‘par’
plotBGpvalues: no visible global function definition for ‘title’
plotBGpvalues: no visible global function definition for ‘axis’
plotBGpvalues: no visible binding for global variable ‘abline’
plotBGpvalues: no visible global function definition for ‘box’
plotCGpvalues: no visible global function definition for ‘par’
plotCGpvalues: no visible global function definition for ‘title’
plotCGpvalues: no visible global function definition for ‘axis’
plotCGpvalues: no visible binding for global variable ‘abline’
plotCGpvalues: no visible global function definition for ‘box’
plotDAGpvalues: no visible global function definition for ‘par’
plotDAGpvalues: no visible global function definition for ‘title’
plotDAGpvalues: no visible global function definition for ‘axis’
plotDAGpvalues: no visible binding for global variable ‘abline’
plotDAGpvalues: no visible global function definition for ‘box’
plotUGpvalues: no visible global function definition for ‘par’
plotUGpvalues: no visible global function definition for ‘title’
plotUGpvalues: no visible global function definition for ‘axis’
plotUGpvalues: no visible binding for global variable ‘abline’
plotUGpvalues: no visible global function definition for ‘box’
simpvalueVec: no visible binding for global variable ‘pnorm’
sinBG: no visible global function definition for ‘cov2cor’
sinCG : sinAMP: no visible global function definition for ‘cov2cor’
sinCG : sinLWF: no visible global function definition for ‘cov2cor’
sinDAG: no visible global function definition for ‘cov2cor’
sinUG: no visible global function definition for ‘cov2cor’
Undefined global functions or variables:
  abline axis box cov2cor par pnorm title
Consider adding
  importFrom("graphics", "abline", "axis", "box", "par", "title")
  importFrom("stats", "cov2cor", "pnorm")
to your NAMESPACE file.
assimilation: no visible global function definition for ‘as.im’
assimilation: no visible global function definition for ‘as.mask’
assimilation: no visible global function definition for ‘coords’
assimilation: no visible global function definition for ‘npoints’
assimilation: no visible global function definition for ‘marks<-’
assimilation_pix: no visible global function definition for ‘as.im’
assimilation_pix: no visible global function definition for ‘as.mask’
assimilation_pix: no visible global function definition for ‘coords’
assimilation_pix: no visible global function definition for ‘npoints’
assimilation_pix: no visible global function definition for ‘eval.im’
assimilation_pix: no visible global function definition for
  ‘integral.im’
assimilation_pix: no visible global function definition for ‘marks<-’
core: no visible global function definition for ‘inside.owin’
core: no visible global function definition for ‘erosion’
core: no visible global function definition for ‘as.owin’
edges: no visible global function definition for ‘erosion’
edges: no visible global function definition for ‘as.owin’
edges: no visible global function definition for ‘periodify’
edges: no visible global function definition for ‘dilation’
pairwise : cindexf: no visible global function definition for ‘npoints’
pairwise : cindexf: no visible global function definition for ‘marks’
pairwise: no visible global function definition for ‘marks’
pairwise: no visible global function definition for ‘marks<-’
pairwise: no visible global function definition for ‘applynbd’
Undefined global functions or variables:
  applynbd as.im as.mask as.owin coords dilation erosion eval.im
  inside.owin integral.im marks marks<- npoints periodify
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘psych’ ‘stringr’
  All declared Imports should be used.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   7.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Undeclared package ‘ranger’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lubridate’ ‘rmarkdown’ ‘yaml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Running examples in ‘sitreeE-Ex.R’ failed
The error most likely occurred in:

> ### Name: PlotDataToLong
> ### Title: Convert Plot data to a data.frame/data.table format
> ### Aliases: PlotDataToLong
> 
> ### ** Examples
> 
> library(sitree)
Loading required package: ggplot2
> 
> result.sitree <- sitree (tree.df   = tr,stand.df  = fl,
+                          functions = list(fn.growth     ='grow.dbhinc.hgtinc',
+                                           fn.mort       ='mort.B2007',
+                                           fn.recr       ='recr.BBG2008',
+                                           fn.management ='management.prob',
+                                           fn.tree.removal ='mng.tree.removal',
+                                           fn.modif      = NULL,
+                                           fn.prep.common.vars ='prep.common.vars.fun'),
+                          n.periods = 5,
+                          period.length = 5,mng.options = NA,
+                          print.comments = FALSE,
+                          fn.dbh.inc = "dbhi.BN2009",
+                          fn.hgt.inc =  "height.korf",
+                          species.spruce = c(1, 2, 3),
+                          species.pine = c(10, 11, 20, 21, 29),species.harw = c(30, 31),
+                          fun.final.felling = "harv.prob",
+                          fun.thinning      = "thin.prob",per.vol.harv = 0.83)
Error in tr$data[["dbh.mm"]][, this.period] : 
  incorrect number of dimensions
Calls: sitree -> do.call -> prep.common.vars.fun
Execution halted
Running examples in ‘sitree-Ex.R’ failed
The error most likely occurred in:

> ### Name: recover.last.measurement
> ### Title: Recover dbh and height at time of death
> ### Aliases: recover.last.measurement
> 
> ### ** Examples
> 
> set.seed(2017)
> res <- sitree (tree.df   = tr,
+                 stand.df  = fl,
+                 functions = list(
+                     fn.growth     = 'grow.dbhinc.hgtinc',
+                     fn.mort       = 'mort.B2007',
+                     fn.recr       = 'recr.BBG2008',
+                     fn.management = 'management.prob',
+                     fn.tree.removal = 'mng.tree.removal',
+                     fn.modif      = NULL, #'ext.modif.fun',
+                     fn.prep.common.vars = 'prep.common.vars.fun'
+                 ),
+                 n.periods = 5,
+                 period.length = 5,
+                 mng.options = NA,
+                 print.comments = FALSE,
+ 		fn.dbh.inc = "dbhi.BN2009",
+                 fn.hgt.inc =  "height.korf", 
+                 species.spruce = c(1, 2, 3),
+                 species.pine = c(10, 11, 20, 21, 29),
+                 species.harw = c(30, 31),
+                 fun.final.felling = "harv.prob",
+                 fun.thinning      = "thin.prob",
+                 'BN2009',
+                 'BBG2008', 'SBA.m2.ha', 'spp','pr.spru.ba', 'QMD.cm',
+                 per.vol.harv = 0.83
+                 )
Error in tr$data[["dbh.mm"]][, this.period] : 
  incorrect number of dimensions
Calls: sitree -> do.call -> prep.common.vars.fun
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘SiTree.Rmd’ using rmarkdown
Quitting from lines 120-140 (SiTree.Rmd) 
Error: processing vignette 'SiTree.Rmd' failed with diagnostics:
incorrect number of dimensions
--- failed re-building ‘SiTree.Rmd’

--- re-building ‘TestEquations.Rmd’ using rmarkdown
Quitting from lines 79-158 (TestEquations.Rmd) 
Error: processing vignette 'TestEquations.Rmd' failed with diagnostics:
incorrect number of dimensions
--- failed re-building ‘TestEquations.Rmd’

SUMMARY: processing the following files failed:
  ‘SiTree.Rmd’ ‘TestEquations.Rmd’

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cvskda: no visible global function definition for ‘detectCores’
cvskda: no visible global function definition for ‘makeCluster’
cvskda: no visible global function definition for ‘clusterApplyLB’
cvskda: no visible global function definition for ‘mclapply’
cvskda: no visible global function definition for ‘stopCluster’
Undefined global functions or variables:
  clusterApplyLB detectCores makeCluster mclapply stopCluster
File ‘skda/libs/skda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘CompQuadForm’ ‘Hmisc’ ‘boot’ ‘mvtnorm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running examples in ‘skewlmm-Ex.R’ failed
The error most likely occurred in:

> ### Name: criteria
> ### Title: Extracts criteria for model comparison of SMSN/SMN objects
> ### Aliases: criteria
> ### Keywords: models
> 
> ### ** Examples
> 
> fm_norm <- smn.lmm(nlme::Orthodont, formFixed = distance ~ age+Sex, groupVar = "Subject")
Iteration  1 
Iteration  2 
Iteration  3 
Iteration  4 
> fm_t <- update(fm_norm, distr="t")
Iteration  1 
Iteration  2 
Iteration  3 
Iteration  4 
Iteration  5 
Iteration  6 
Iteration  7 
Iteration  8 
Iteration  9 
Iteration  10 
Iteration  11 
Iteration  12 
Iteration  13 
Iteration  14 
Iteration  15 
Iteration  16 
Iteration  17 
Iteration  18 
Iteration  19 
> fm_sn<- smsn.lmm(nlme::Orthodont, formFixed = distance ~ age+Sex, groupVar = "Subject")
Warning in mean.default(x) :
  argument is not numeric or logical: returning NA
Warning in mean.default(x) :
  argument is not numeric or logical: returning NA
Error in if ((t(Deltab) %*% sD1 %*% Deltab) >= 1) Deltab <- Deltab/as.numeric(sqrt(t(Deltab) %*%  : 
  missing value where TRUE/FALSE needed
Calls: smsn.lmm ... DAAREM.SkewUNC -> daarem -> daarem_base_objfn -> fixptfn
Execution halted
dskt: no visible global function definition for ‘dt’
pskt: no visible global function definition for ‘pt’
qskt: no visible global function definition for ‘qt’
rskt: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘kmndirs’
Unavailable namespace imported from by a ':::' call: ‘kmndirs’
  See the note in ?`:::` about the use of this operator.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.8Mb
GNU make is a SystemRequirements.
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 36.5Mb
  sub-directories of 1Mb or more:
    libs  34.9Mb
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘numDeriv’ ‘png’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RcppArmadillo’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Note: found 23 marked UTF-8 strings
slcestimates: no visible global function definition for ‘par’
slcestimates: no visible global function definition for ‘abline’
slcestimates: no visible global function definition for ‘lines’
slcestimates: no visible global function definition for ‘axis’
slcestimates: no visible global function definition for ‘points’
slcestimates: no visible global function definition for ‘title’
Undefined global functions or variables:
  abline axis lines par points title
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "par", "points",
             "title")
to your NAMESPACE file.
Undeclared package ‘RcmdrPlugin.SLC’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
File ‘SLHD/libs/SLHD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘viridisLite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Note: found 2 marked Latin-1 strings
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.
'LazyData' is specified without a 'data' directory
Note: found 15 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
Undeclared packages ‘InformationValue’, ‘ggthemes’ in Rd xrefs
Note: found 1122 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘covr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘mice’ in Rd xrefs
File ‘smco/R/smco.R’:
  .onAttach calls:
    cat(paste("This is smco package", version, "\n"))

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

smco: no visible global function definition for ‘runif’
smco: no visible global function definition for ‘rnorm’
smco: no visible global function definition for ‘qnorm’
smco: no visible global function definition for ‘pnorm’
smco: no visible global function definition for ‘optim’
Undefined global functions or variables:
  optim pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "optim", "pnorm", "qnorm", "rnorm", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Non-standard file/directory found at top level:
  ‘etc’
File ‘SMC/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("##\n", "## Sequential Monte Carlo Package (SMC)\n",     "##\n", "## Functionality: sequential Monte Carlo (SMC) or sequential importance\n",     "## sampling (SIS) or hidden Markov models (HMM), particle filter (PF)\n",     "## and auxiliary particle filter (APF)\n", "##\n", "## Use: \"help(package = SMC)\" at the R prompt for more info\n",     "##\n", "## Copyright (C) 2006-", this.year, " Gopi Goswami\n",     "##\n", "##    Created by: Gopi Goswami <goswami@stat.harvard.edu>\n",     "## Maintained by: Gopi Goswami <grgoswami@gmail.com>\n",     "##\n")

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
em: no visible global function definition for ‘coxph’
em: no visible global function definition for ‘optim’
plotpredictsmcure: no visible global function definition for ‘matplot’
plotpredictsmcure: no visible global function definition for ‘lines’
smcure: no visible binding for global variable ‘na.omit’
smcure: no visible global function definition for ‘model.frame’
smcure: no visible global function definition for ‘model.extract’
smcure: no visible global function definition for ‘model.matrix’
smcure: no visible global function definition for ‘coxph’
smcure: no visible global function definition for ‘survreg’
smcure: no visible binding for global variable ‘var’
smcure: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  coxph lines matplot model.extract model.frame model.matrix na.omit
  optim pnorm survreg var
Consider adding
  importFrom("graphics", "lines", "matplot")
  importFrom("stats", "model.extract", "model.frame", "model.matrix",
             "na.omit", "optim", "pnorm", "var")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Grad.sph: no visible global function definition for ‘dist’
IMDS: no visible global function definition for ‘cmdscale’
IMDS: no visible global function definition for ‘as.dist’
IMDS: no visible global function definition for ‘runif’
IMDS: no visible global function definition for ‘optim’
idistSph: no visible global function definition for ‘dist’
obj.sph: no visible global function definition for ‘dist’
plot.imds: no visible binding for global variable ‘lines’
plot.imds: no visible global function definition for ‘text’
plot.imds: no visible global function definition for ‘rect’
Undefined global functions or variables:
  as.dist cmdscale dist lines optim rect runif text
Consider adding
  importFrom("graphics", "lines", "rect", "text")
  importFrom("stats", "as.dist", "cmdscale", "dist", "optim", "runif")
to your NAMESPACE file.
File ‘smds/libs/smds.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘ggplot2’ ‘reshape’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘corpcor’ ‘ggplot2’ ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
lines.SmithWilsonYieldCurve: no visible global function definition for
  ‘lines’
points.SmithWilsonYieldCurve: no visible global function definition for
  ‘points’
Undefined global functions or variables:
  lines points
Consider adding
  importFrom("graphics", "lines", "points")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rPython’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    3.8Mb
    libs  10.9Mb
'LazyData' is specified without a 'data' directory
Running examples in ‘smoothROCtime-Ex.R’ failed
The error most likely occurred in:

> ### Name: funcen
> ### Title: Bivariate kernel density estimation under random censoring
> ### Aliases: funcen
> 
> ### ** Examples
> 
> library(smoothROCtime)
> require(KMsurv)
Loading required package: KMsurv
> require(lattice)
Loading required package: lattice
> 
> data(kidtran)
> 
> # Preparing data: a logarithmic transformationof the time-to-event variable is made
>   DT <- cbind(log(kidtran$time),kidtran$delta,kidtran$age)
>   n  <-length(log(kidtran$time))
> 
> # Directly definition of the bandwidth matrix
>   H  <- diag((c(sd(kidtran$age),sd(log(kidtran$time)))*n^(-0.2))^2)
> 
> # Kernel density function estimation
>   density <- funcen(data=DT,H=H)
========================================
                                        
================================================================================
Warning in sweep(x, 2, mu) :
  STATS does not recycle exactly across MARGIN
Error in x %*% Ginv : non-conformable arguments
Calls: funcen ... kdde.binned.nd -> dmvnorm.deriv -> do.call -> dmvnorm.deriv.unique
Execution halted
Namespaces in Imports field not imported from:
  ‘methods’ ‘rgeos’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
Found the following files/directories:
  ‘my_new_social_media_plot.png’
Malformed Description field: should contain one or more complete sentences.
dNMR: no visible global function definition for ‘pnorm’
dNMR: no visible global function definition for ‘dnorm’
pNMR: no visible global function definition for ‘pnorm’
pNMR: no visible global function definition for ‘dnorm’
rMR: no visible global function definition for ‘rnorm’
rMR: no visible global function definition for ‘rchisq’
Undefined global functions or variables:
  dnorm pnorm rchisq rnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm", "rchisq", "rnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
SMVar.paired : <anonymous>: no visible global function definition for
  ‘var’
SMVar.paired: no visible global function definition for ‘var’
SMVar.paired: no visible global function definition for ‘pt’
SMVar.paired: no visible global function definition for ‘p.adjust’
SMVar.paired: no visible global function definition for ‘write.table’
SMVar.unpaired : <anonymous>: no visible global function definition for
  ‘var’
SMVar.unpaired: no visible global function definition for ‘var’
SMVar.unpaired: no visible global function definition for ‘pt’
SMVar.unpaired: no visible global function definition for ‘p.adjust’
SMVar.unpaired: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  p.adjust pt var write.table
Consider adding
  importFrom("stats", "p.adjust", "pt", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Rd file 'SMVar.paired.Rd':
  \usage lines wider than 90 characters:
     SMVar.paired(geneNumbers, logratio, fileexport = NULL, minrep = 2, method = "BH", threshold = 0.05)

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

These lines will be truncated in the PDF manual.
Undeclared package ‘andrews’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Package in Depends field not imported from: ‘snow’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
KS.test: no visible global function definition for ‘quantile’
KS.test : Fgaus: no visible global function definition for ‘pnorm’
KS.test: no visible global function definition for ‘setNames’
cs.test: no visible global function definition for ‘pbinom’
cs.test: no visible global function definition for ‘pnorm’
cs.test: no visible global function definition for ‘setNames’
kde: no visible global function definition for ‘quantile’
kde : Fgaus: no visible global function definition for ‘pnorm’
kde: no visible global function definition for ‘par’
kre: no visible global function definition for ‘quantile’
kre: no visible global function definition for ‘lines’
ns.test: no visible global function definition for ‘complete.cases’
ns.test: no visible global function definition for ‘qnorm’
ns.test: no visible global function definition for ‘pnorm’
ns.test: no visible global function definition for ‘pchisq’
ns.test: no visible global function definition for ‘setNames’
ns.test: no visible global function definition for ‘qt’
quant.test: no visible global function definition for ‘complete.cases’
quant.test: no visible global function definition for ‘pbinom’
quant.test: no visible global function definition for ‘pnorm’
quant.test: no visible global function definition for ‘setNames’
quant.test: no visible global function definition for ‘quantile’
quant.test: no visible global function definition for ‘phyper’
runs.test: no visible global function definition for ‘median’
runs.test: no visible global function definition for ‘setNames’
runs.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  complete.cases lines median par pbinom pchisq phyper pnorm qnorm qt
  quantile setNames
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "complete.cases", "median", "pbinom", "pchisq",
             "phyper", "pnorm", "qnorm", "qt", "quantile", "setNames")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.3Mb
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘mvtnorm’ ‘combinat’
A package should be listed in only one of these fields.
chisq.test.a: no visible global function definition for ‘chisq.test’
maxsel: no visible global function definition for ‘complete.cases’
maxsel.asymp.test: no visible global function definition for
  ‘complete.cases’
Undefined global functions or variables:
  chisq.test complete.cases
Consider adding
  importFrom("stats", "chisq.test", "complete.cases")
to your NAMESPACE file.
Package in Depends field not imported from: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages in Depends field not imported from:
  ‘colorspace’ ‘snpStats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
check.args: no visible global function definition for ‘is’
write.sbams: no visible global function definition for ‘as’
write.sbams: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  as is write.table
Consider adding
  importFrom("methods", "as", "is")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘snpStatsWriter/libs/snpStatsWriter.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘.R_Test’
Namespaces in Imports field not imported from:
  ‘devtools’ ‘raster’ ‘rlang’ ‘sp’ ‘usethis’
  All declared Imports should be used.
Running ‘testthat.R’ [10s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sobir)
  > 
  > test_check("sobir")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (tests.R:42:3): perm_area should calculate the no-data zone areas for each permutation of the data simulated nsim times ──
  bperm$data[6, 4] is not strictly more than 0.5. Difference: -0.473
  ── Failure (tests.R:54:3): perm_plot should pull the appropriate data from the perm_area analysis ──
  bpplot$data[5, 4] is not strictly more than 0.6. Difference: -0.376
  
  [ FAIL 2 | WARN 2 | SKIP 0 | PASS 6 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘flextable’ ‘htmlTable’ ‘stringr’
  All declared Imports should be used.
Note: found 938 marked UTF-8 strings
Malformed Title field: should not end in a period.
calculate.areas: no visible global function definition for ‘runif’
calculate.gradedareas: no visible global function definition for
  ‘rnorm’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
File ‘SocialNetworks/libs/SocialNetworks.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘GeneralModel.Rnw’ using Sweave
Loading required package: deSolve
Loading required package: parallel
Loading required package: RUnit
--- finished re-building ‘GeneralModel.Rnw’

--- re-building ‘ParameterEstimation.Rnw’ using Sweave
Loading required package: rootSolve
Loading required package: coda

Error: processing vignette 'ParameterEstimation.Rnw' failed with diagnostics:
 chunk 5 
Error in xy.coords(x, y, setLab = FALSE) : 
  'list' object cannot be coerced to type 'double'

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘soiltexture_vignette.Rnw’ using Sweave

Error: processing vignette 'soiltexture_vignette.Rnw' failed with diagnostics:
 chunk 80 
Error in FUN(x, aperm(array(STATS, dims[perm]), order(perm)), ...) : 
  non-numeric argument to binary operator

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘lgr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Undeclared package ‘XML’ in Rd xrefs
soma: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
bm: no visible global function definition for ‘rnorm’
bm: no visible global function definition for ‘ts’
fbm: no visible global function definition for ‘fft’
fbm: no visible global function definition for ‘rnorm’
fbm: no visible global function definition for ‘ts’
gbm: no visible global function definition for ‘rnorm’
gbm: no visible global function definition for ‘ts’
Undefined global functions or variables:
  fft rnorm ts
Consider adding
  importFrom("stats", "fft", "rnorm", "ts")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
getAlpha: no visible global function definition for ‘pbinom’
kfweOrd: no visible global function definition for ‘qnbinom’
Undefined global functions or variables:
  pbinom qnbinom
Consider adding
  importFrom("stats", "pbinom", "qnbinom")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘rlist’
  All declared Imports should be used.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    2.2Mb
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘hexbin’ which was already attached by Depends.
  Please remove these calls from your code.
hexbinpie: no visible global function definition for ‘quantile’
hexbinpie: no visible global function definition for ‘polygon’
hexbinpie: no visible global function definition for ‘text’
makehexbinplot: no visible global function definition for ‘rainbow’
makehexbinplot: no visible global function definition for ‘col2rgb’
makehexbinplot: no visible global function definition for ‘edit’
makehexbinplot: no visible global function definition for ‘dev.new’
makehexbinplot: no visible global function definition for ‘plot.new’
makehexbinplot: no visible global function definition for ‘plot.window’
makehexbinplot: no visible global function definition for ‘box’
makehexbinplot: no visible global function definition for ‘axis’
makehexbinplot: no visible global function definition for ‘legend’
som.plot: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  axis box col2rgb dev.new edit legend plot.new plot.window polygon
  quantile rainbow read.table text
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new", "rainbow")
  importFrom("graphics", "axis", "box", "legend", "plot.new",
             "plot.window", "polygon", "text")
  importFrom("stats", "quantile")
  importFrom("utils", "edit", "read.table")
to your NAMESPACE file.
File ‘som/libs/som.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
convert_municipality_names: no visible global function definition for
  ‘read.csv’
regression_plot: no visible binding for global variable ‘loess’
regression_plot: no visible global function definition for
  ‘colorRampPalette’
regression_plot: no visible global function definition for
  ‘loess.control’
regression_plot: no visible global function definition for ‘predict’
regression_plot : <anonymous>: no visible global function definition
  for ‘quantile’
regression_plot : <anonymous>: no visible global function definition
  for ‘pnorm’
regression_plot: no visible global function definition for
  ‘flush.console’
regression_plot: no visible global function definition for ‘density’
Undefined global functions or variables:
  colorRampPalette density flush.console loess loess.control pnorm
  predict quantile read.csv
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "density", "loess", "loess.control", "pnorm",
             "predict", "quantile")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
Undeclared package ‘testthat’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SciencesPo’
'LazyData' is specified without a 'data' directory
File ‘SoundexBR/libs/SoundexBR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Running examples in ‘soundgen-Ex.R’ failed
The error most likely occurred in:

> ### Name: getCheckerboardKernel
> ### Title: Checkerboard kernel
> ### Aliases: getCheckerboardKernel
> ### Keywords: internal
> 
> ### ** Examples
> 
> kernel = soundgen:::getCheckerboardKernel(size = 64, kernelSD = 0.1, plot = TRUE)
Error in t(x) - mean : non-numeric argument to binary operator
Calls: <Anonymous> -> <Anonymous> -> backsolve
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘acoustic_analysis.Rmd’ using rmarkdown
Quitting from lines 709-717 (acoustic_analysis.Rmd) 
Error: processing vignette 'acoustic_analysis.Rmd' failed with diagnostics:
Failed to analyze any input
--- failed re-building ‘acoustic_analysis.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.1Mb
Namespaces in Imports field not imported from:
  ‘gtools’ ‘reshape2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘r2cytoscape’
Running examples in ‘SourceSet-Ex.R’ failed
The error most likely occurred in:

> ### Name: infoSource
> ### Title: Get summary statistics on graphs and variables
> ### Aliases: infoSource
> 
> ### ** Examples
> 
> ## Load the SourceSetObj obtained from the source set analysis of ALL dataset
> 
> # see vignette for more details
> print(load(file=system.file("extdata","ALLsourceresult.RData",package = "SourceSet")))
[1] "results.all"
> class(results.all)
[1] "sourceSetList"
> 
> info.all<-infoSource(sourceObj = results.all)
Loading required package: graph
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

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

    IQR, mad, sd, var, xtabs

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

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

Warning in `[.data.frame`(x$env$data, 1L, drop = FALSE) :
  'drop' argument will be ignored
Error in .subset2(x, i, exact = exact) : subscript out of bounds
Calls: infoSource ... <Anonymous> -> .fun -> [[ -> [[.data.frame -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘SourceSet.Rmd’ using rmarkdown
Loading required package: graph
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

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

Identifing all possible orderings..
Total run time: 5.67 secs
Quitting from lines 257-259 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘SourceSet.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
'LazyData' is specified without a 'data' directory
exploreSP23Design: no visible global function definition for
  ‘txtProgressBar’
exploreSP23Design: no visible global function definition for
  ‘setTxtProgressBar’
generateClinicalTrialData : <anonymous>: no visible global function
  definition for ‘runif’
generateClinicalTrialData: no visible global function definition for
  ‘rbinom’
generateClinicalTrialData: no visible global function definition for
  ‘rexp’
mHP.b : crossingProbDiff: no visible global function definition for
  ‘pnorm’
mHP.b : crossingProbDiff: no visible global function definition for
  ‘Miwa’
mHP.b: no visible global function definition for ‘qnorm’
mHP.b: no visible global function definition for ‘uniroot’
mHP.c : crossingProbDiff: no visible global function definition for
  ‘Miwa’
mHP.c: no visible global function definition for ‘uniroot’
mHP.c: no visible global function definition for ‘qnorm’
performInterimLook: no visible global function definition for ‘optim’
performInterimLook: no visible global function definition for
  ‘constrOptim’
performInterimLook: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  Miwa constrOptim optim pnorm qnorm rbinom rexp runif
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("stats", "constrOptim", "optim", "pnorm", "qnorm", "rbinom",
             "rexp", "runif", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
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.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    include   2.1Mb
    libs      2.9Mb
'LazyData' is specified without a 'data' directory
Rd file 'space.joint.Rd':
  \examples lines wider than 100 characters:
     #################### view the network corresponding to the parcial correlation matrix in the simulation example
     #plot(temp, vertex.size=3, vertex.frame.color="white",layout=layout.fruchterman.reingold, vertex.label=NA, edge.color=grey(0.5))

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘spacesRGB-guide.Rmd’ using rmarkdown
Error reading bibliography file bibliography.bib:
(line 533, column 9):
unexpected '['
Error: processing vignette 'spacesRGB-guide.Rmd' failed with diagnostics:
pandoc document conversion failed with error 25
--- failed re-building ‘spacesRGB-guide.Rmd’

SUMMARY: processing the following file failed:
  ‘spacesRGB-guide.Rmd’

Error: Vignette re-building failed.
Execution halted
Undeclared package ‘colorSpec’ in Rd xrefs
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Undeclared package ‘rebus.base’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘rstudioapi’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running examples in ‘spagmix-Ex.R’ failed
The error most likely occurred in:

> ### Name: lgcpmix
> ### Title: Generate a spatial log-Gaussian Cox process intensity
> ### Aliases: lgcpmix
> 
> ### ** Examples
> 
> ## Homogeneous example ##
> 
> # Create constant intensity image integrating to 500
> 
> homog <- as.im(as.mask(toywin))
> homog <- homog/integral(homog)*500
> 
> 
> # Corresponding LGCP realisations using exponential covariance structure
> par(mfrow=c(2,2),mar=rep(1.5,4))
> for(i in 1:4){
+   temp <- lgcpmix(homog,covmod="exp",covpars=list(var=1,scale=0.2))
+   plot(temp,main=paste("Realisation",i),log=TRUE)
+ }
> 
> 
> 
> ## Inhomogeneous examples ##
> 
> # Create deterministic trend
> 
> mn <- cbind(c(0.25,0.8),c(0.31,0.82),c(0.43,0.64),c(0.63,0.62),c(0.21,0.26))
> v1 <- matrix(c(0.0023,-0.0009,-0.0009,0.002),2)
> v2 <- matrix(c(0.0016,0.0015,0.0015,0.004),2)
> v3 <- matrix(c(0.0007,0.0004,0.0004,0.0011),2)
> v4 <- matrix(c(0.0023,-0.0041,-0.0041,0.0099),2)
> v5 <- matrix(c(0.0013,0.0011,0.0011,0.0014),2)
> vr <- array(NA,dim=c(2,2,5))
> for(i in 1:5) vr[,,i] <- get(paste("v",i,sep=""))
> intens <- sgmix(mean=mn,vcv=vr,window=toywin,p0=0.1,int=500)
Error in t(x) - mean : non-numeric argument to binary operator
Calls: sgmix -> dmvnorm -> backsolve
Execution halted
installed size is 36.6Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs  33.4Mb
Running examples in ‘spaMM-Ex.R’ failed
The error most likely occurred in:

> ### Name: fix_predVar
> ### Title: Prediction from models with nearly-singular covariance matrices
> ### Aliases: fix_predVar
> 
> ### ** Examples
> 
> data("blackcap")
> fitobject <- corrHLfit(migStatus ~ 1 + Matern(1|longitude+latitude),data=blackcap,
+                        ranFix=list(nu=10,rho=0.001)) ## numerically singular C
> get_predVar(fitobject,newdata=blackcap[6,]) 
Error in .get_locdata(newdata, locform = locform, object = object, variances = variances) : 
  (!) newdata has incorrect length. It should match the following variables:
 longitude latitude
Calls: get_predVar ... <Anonymous> -> .predict_body -> .calc_new_X_ZAC -> .get_locdata
Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
hausman: no visible global function definition for ‘pchisq’
span.formula: no visible global function definition for ‘model.frame’
span.formula: no visible global function definition for ‘model.matrix’
span.formula: no visible global function definition for
  ‘model.response’
spbe: no visible global function definition for ‘cor’
spbe: no visible global function definition for ‘pt’
spfe: no visible global function definition for ‘cor’
spfe: no visible global function definition for ‘pt’
sprandom: no visible global function definition for ‘cor’
sprandom: no visible global function definition for ‘pt’
summary.span: no visible global function definition for ‘printCoefmat’
Undefined global functions or variables:
  cor model.frame model.matrix model.response pchisq printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "pchisq", "printCoefmat", "pt")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
File ‘sparcl/libs/sparcl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    java   3.4Mb
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages in Depends field not imported from:
  ‘RCurl’ ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPARQL : <anonymous>: no visible global function definition for
  ‘URLencode’
SPARQL: no visible binding for global variable ‘getURL’
SPARQL: no visible global function definition for ‘URLencode’
SPARQL: no visible binding for global variable ‘xmlParse’
SPARQL: no visible global function definition for ‘getNodeSet’
SPARQL: no visible global function definition for ‘xpathApply’
SPARQL: no visible binding for global variable ‘postForm’
get_attr: no visible global function definition for ‘getNodeSet’
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for ‘getNodeSet’
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for ‘xmlDoc’
get_value: no visible global function definition for ‘xmlDoc’
get_value: no visible global function definition for ‘xpathSApply’
get_value: no visible binding for global variable ‘xmlValue’
get_value: no visible global function definition for ‘xpathApply’
get_value: no visible binding for global variable ‘xmlGetAttr’
readCSVstring: no visible global function definition for ‘read.csv’
readTSVstring: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  URLencode getNodeSet getURL postForm read.csv read.delim xmlDoc
  xmlGetAttr xmlParse xmlValue xpathApply xpathSApply
Consider adding
  importFrom("utils", "URLencode", "read.csv", "read.delim")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
f.I2.cont: no visible global function definition for ‘combn’
f.I2.dich: no visible global function definition for ‘combn’
f.pstar.cont: no visible global function definition for ‘combn’
f.pstar.dich: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Undeclared packages ‘splancs’, ‘spatstat.data’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘gtable’ ‘rlang’ ‘testthat’
  All declared Imports should be used.
Undeclared package ‘sparsebn’ in Rd xrefs
Running examples in ‘sparsediscrim-Ex.R’ failed
The error most likely occurred in:

> ### Name: lda_diag
> ### Title: Diagonal Linear Discriminant Analysis (DLDA)
> ### Aliases: lda_diag lda_diag.default lda_diag.formula predict.lda_diag
> 
> ### ** Examples
> 
> library(modeldata)
> data(penguins)
> pred_rows <- seq(1, 344, by = 20)
> penguins <- penguins[, c("species", "body_mass_g", "flipper_length_mm")]
> dlda_out <- lda_diag(species ~ ., data = penguins[-pred_rows, ])
> predicted <- predict(dlda_out, penguins[pred_rows, -1], type = "class")
> 
> dlda_out2 <- lda_diag(x = penguins[-pred_rows, -1], y = penguins$species[-pred_rows])
Error: 'x' should be a matrix or data frame.
Backtrace:
    █
 1. ├─sparsediscrim::lda_diag(x = penguins[-pred_rows, -1], y = penguins$species[-pred_rows])
 2. └─sparsediscrim:::lda_diag.default(...)
 3.   └─sparsediscrim:::pred_to_matrix(x)
Execution halted
'LazyData' is specified without a 'data' directory
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.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  15.1Mb
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.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘future’ ‘geosphere’ ‘lubridate’ ‘tidyverse’ ‘viridis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
Malformed Description field: should contain one or more complete sentences.
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.
'LazyData' is specified without a 'data' directory
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.
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘spatstat.linnet’
  All declared Imports should be used.
Running examples in ‘SpatEntropy-Ex.R’ failed
The error most likely occurred in:

> ### Name: raintrees
> ### Title: Rainforest tree data.
> ### Aliases: raintrees
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(raintrees)
> #plot(raintrees, main="", pch=16, cols=1:4)
> 
> #shannon's entropy of the four trees
> shannon(raintrees)
Error in order(y) : unimplemented type 'list' in 'orderVector1'
Calls: shannon -> prop.table -> table -> factor -> order
Execution halted
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘irlba’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    help   1.7Mb
Note: found 283 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ggpubr’ ‘pheatmap’ ‘rlist’ ‘stats’ ‘viridis’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  21.7Mb
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.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      3.2Mb
    help   3.2Mb
    libs   1.1Mb
Running examples in ‘spatstat.geom-Ex.R’ failed
The error most likely occurred in:

> ### Name: by.ppp
> ### Title: Apply a Function to a Point Pattern Broken Down by Factor
> ### Aliases: by.ppp
> ### Keywords: spatial methods manip
> 
> ### ** Examples
> 
>   # multitype point pattern, broken down by type
>   data(amacrine)
>   by(amacrine, FUN=minnndist)
off:
[1] 0.02486202

on:
[1] 0.03218897
>   by(amacrine, FUN=function(x) { intensity(unmark(x)) })
off:
[1] 88.68302

on:
[1] 94.9283
> 
>   if(require(spatstat.core)) {
+   # how to pass additional arguments to FUN
+   by(amacrine, FUN=clarkevans, correction=c("Donnelly","cdf"))
+   }
Loading required package: spatstat.core
Loading required package: nlme
Loading required package: rpart
spatstat.core 2.3-2
off:
Donnelly      cdf 
1.476458 1.465373 

on:
Donnelly      cdf 
1.406853 1.427163 
> 
>   # point pattern broken down by tessellation
>   data(swedishpines)
>   tes <- quadrats(swedishpines, 4,4)
>   ## compute minimum nearest neighbour distance for points in each tile
>   B <- by(swedishpines, tes, minnndist)
Error in cut.ppp(x, fsplit) : length(z) == npoints(x) is not TRUE
Calls: by ... split -> split.ppp -> marks -> cut -> cut.ppp -> stopifnot
Execution halted
Depends: includes the non-default packages:
  'spatstat.geom', 'spatstat.core', 'spatstat.linnet', 'spatstat.data',
  'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Namespace in Imports field not imported from: ‘spatstat’
  All declared Imports should be used.
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    libs  27.2Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   9.0Mb
Running examples in ‘spc4sts-Ex.R’ failed
The error most likely occurred in:

> ### Name: showNb
> ### Title: Show Neighborhood
> ### Aliases: showNb
> 
> ### ** Examples
> 
> ## show the neighorhood with variables names of the data frame constructed by dataPrep()
> img <- matrix(1:25, 5, 5) # an image of size 5x5 pixels
> img
     [,1] [,2] [,3] [,4] [,5]
[1,]    1    6   11   16   21
[2,]    2    7   12   17   22
[3,]    3    8   13   18   23
[4,]    4    9   14   19   24
[5,]    5   10   15   20   25
> dataPrep(img, 2)
  V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 V13
1 13  1  2  3  6  7  8 11 12  16  17  21  22
2 14  2  3  4  7  8  9 12 13  17  18  22  23
3 15  3  4  5  8  9 10 13 14  18  19  23  24
> showNb(c(2, 2, 2)) # showNb(2) has the same effect
> 
> ## show the neighorhood with predictors and their importance used in the model returned
> ## by surfacemodel()
> img <- sarGen(m = 100, n = 100, border = 50) # training image
> model <- surfacemodel(img, nb = 3)
> showNb(model, "predictors") # show predictors
Error in showNb(model, "predictors") : 
  Wrong input for the model argument!
Execution halted
Running examples in ‘spcadjust-Ex.R’ failed
The error most likely occurred in:

> ### Name: SPCModellogregLikRatio
> ### Title: Data Model for Binary Responses using a logarithmic model and
> ###   likelihood ratio updates.
> ### Aliases: SPCModellogregLikRatio
> 
> ### ** Examples
> 
> n <- 1000
> Xlogreg <- data.frame(x1=rbinom(n,1,0.4), x2=runif(n,0,1), x3=rnorm(n))
> xbeta <- -1+Xlogreg$x1*100+Xlogreg$x2+Xlogreg$x3
> Xlogreg$y <- rbinom(n,1,exp(xbeta)/(1+exp(xbeta)))
> chartlogreg <- new("SPCCUSUM",
+                    model=SPCModellogregLikRatio(Delta= 1, formula="y~x1+x2+x3"))
> SPCproperty(data=Xlogreg,nrep=10,property="calARL",
+             chart=chartlogreg,params=list(target=100))

  |                                                                            
  |                                                                      |   0%Error in eval(predvars, data, env) : object 'y' not found
Calls: SPCproperty ... eval -> <Anonymous> -> model.frame.default -> eval -> eval
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘CUSUM_LinearRegression.Rmd’ using knitr
Quitting from lines 54-58 (CUSUM_LinearRegression.Rmd) 
Error: processing vignette 'CUSUM_LinearRegression.Rmd' failed with diagnostics:
object 'y' not found
--- failed re-building ‘CUSUM_LinearRegression.Rmd’

--- re-building ‘CUSUM_LogisticRegression.Rmd’ using knitr
Quitting from lines 66-70 (CUSUM_LogisticRegression.Rmd) 
Error: processing vignette 'CUSUM_LogisticRegression.Rmd' failed with diagnostics:
object 'x1' not found
--- failed re-building ‘CUSUM_LogisticRegression.Rmd’

--- re-building ‘CUSUM_NormalNormal.Rmd’ using knitr
--- finished re-building ‘CUSUM_NormalNormal.Rmd’

--- re-building ‘EWMA_NormalNormal.Rmd’ using knitr
--- finished re-building ‘EWMA_NormalNormal.Rmd’

--- re-building ‘Extensions.Rmd’ using knitr
--- finished re-building ‘Extensions.Rmd’

--- re-building ‘Shewhart_NormalNormal.Rmd’ using knitr
--- finished re-building ‘Shewhart_NormalNormal.Rmd’

SUMMARY: processing the following files failed:
  ‘CUSUM_LinearRegression.Rmd’ ‘CUSUM_LogisticRegression.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
GenerateCliquesCovariance: no visible global function definition for
  ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
File ‘spcr/libs/spcr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘spDataLarge’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
Note: found 56 marked UTF-8 strings
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    help   1.6Mb
Note: found 34 marked UTF-8 strings
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   6.1Mb
    etc   1.4Mb
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
bartlett: no visible global function definition for ‘pchisq’
local.rbfdot: no visible binding for global variable ‘sd’
local.rbfdot: no visible global function definition for ‘dist’
local.rbfdot : <anonymous>: no visible global function definition for
  ‘median’
speccalt: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  dist kmeans median pchisq sd
Consider adding
  importFrom("stats", "dist", "kmeans", "median", "pchisq", "sd")
to your NAMESPACE file.
ChaoBunge: no visible global function definition for ‘qnorm’
ChaoLee1992: no visible global function definition for ‘qnorm’
Pmix: no visible global function definition for ‘dpois’
PmixSCon: no visible global function definition for ‘dbeta’
bootPCG: no visible global function definition for ‘flush.console’
bootPCG: no visible global function definition for ‘quantile’
bootPnpmle: no visible global function definition for ‘flush.console’
bootPnpmle: no visible global function definition for ‘quantile’
bootUnpmle: no visible global function definition for ‘flush.console’
bootUnpmle: no visible global function definition for ‘quantile’
chao1984: no visible global function definition for ‘qnorm’
jackknife: no visible global function definition for ‘dbinom’
jackknife: no visible global function definition for ‘qnorm’
pcg: no visible global function definition for ‘flush.console’
unpmle: no visible global function definition for ‘flush.console’
untrunPmix: no visible global function definition for ‘dpois’
Undefined global functions or variables:
  dbeta dbinom dpois flush.console qnorm quantile
Consider adding
  importFrom("stats", "dbeta", "dbinom", "dpois", "qnorm", "quantile")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
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.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘xcms’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rcytoscapejs’

Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘specmine.datasets’
  All declared Imports should be used.
Undeclared package ‘hyperSpec’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Running examples in ‘spectralGP-Ex.R’ failed
The error most likely occurred in:

> ### Name: add.blocks.gp
> ### Title: Adds coefficient block structure to a spectral GP object
> ### Aliases: add.blocks.gp
> ### Keywords: models smooth spatial
> 
> ### ** Examples
> 
> library(spectralGP)
> gp1=gp(128,matern.specdens,c(1,4))
Note that the spatial range parameter is interpreted based
on the process living on a (0,1)^d grid
> gp2=gp(c(64,64),matern.specdens,c(1,4))
Warning in object$specdens(object$omega, object$specdens.param, d = object$d) :
  Assuming a single two-dimensional frequency.

Error in omega[, 1] * omega[, 1] : 
  non-numeric argument to binary operator
Calls: gp ... calc.variances -> calc.variances.gp -> matrix -> <Anonymous>
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Note: found 5 marked Latin-1 strings
Undeclared package ‘biglm’ in Rd xrefs
'library' or 'require' call to ‘leaps’ which was already attached by Depends.
  Please remove these calls from your code.
modSearch: no visible global function definition for ‘glm’
modSearch: no visible binding for global variable ‘binomial’
modSearch: no visible global function definition for ‘na.omit’
modSearch: no visible global function definition for ‘as.formula’
speff: no visible binding for global variable ‘na.pass’
speff: no visible global function definition for ‘model.matrix’
speff: no visible global function definition for ‘terms’
speff: no visible global function definition for ‘model.response’
speff: no visible global function definition for ‘as.formula’
speff: no visible global function definition for ‘predict’
speff: no visible global function definition for ‘na.omit’
speff: no visible global function definition for ‘glm’
speff: no visible binding for global variable ‘na.omit’
speffSurv: no visible global function definition for ‘model.matrix’
speffSurv: no visible global function definition for ‘terms’
speffSurv: no visible global function definition for ‘model.response’
speffSurv: no visible global function definition for ‘as.formula’
speffSurv: no visible global function definition for ‘uniroot’
summary.speff: no visible global function definition for ‘qnorm’
summary.speff: no visible global function definition for ‘pnorm’
summary.speffSurv: no visible global function definition for ‘qnorm’
summary.speffSurv: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula binomial glm model.matrix model.response na.omit na.pass
  pnorm predict qnorm terms uniroot
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "model.matrix",
             "model.response", "na.omit", "na.pass", "pnorm", "predict",
             "qnorm", "terms", "uniroot")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.neig’
Malformed Description field: should contain one or more complete sentences.
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: ‘mathjaxr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    libs  21.2Mb
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: ‘rgl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pointsphere: no visible global function definition for ‘runif’
rgl.sphMW: no visible global function definition for ‘plot3d’
rgl.sphcirc: no visible global function definition for ‘rotate3d’
rgl.sphcirc: no visible global function definition for ‘lines3d’
rgl.sphgrid: no visible global function definition for ‘open3d’
rgl.sphgrid: no visible global function definition for ‘plot3d’
rgl.sphgrid: no visible global function definition for ‘lines3d’
rgl.sphgrid: no visible global function definition for ‘text3d’
rgl.sphpoints: no visible global function definition for ‘points3d’
rgl.sphsun: no visible global function definition for ‘plot3d’
rgl.sphtext: no visible global function definition for ‘text3d’
Undefined global functions or variables:
  lines3d open3d plot3d points3d rotate3d runif text3d
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
Note: found 189 marked UTF-8 strings
Running examples in ‘sphunif-Ex.R’ failed
The error most likely occurred in:

> ### Name: comets
> ### Title: Comet orbits
> ### Aliases: comets
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # Load data
> data("comets")
> 
> # Add normal vectors
> comets$normal <- cbind(sin(comets$i) * sin(comets$om),
+                        -sin(comets$i) * cos(comets$om),
+                        cos(comets$i))
> 
> # Add numbered information
> comets$numbered <- substr(comets$id, 1, 1) == "c"
> 
> # Tests to be performed
> type_tests <- c("PCvM", "PAD", "PRt")
> 
> # Excluding the C/1882 R1-X (Great September comet) records with X = B, C, D
> comets_ccf2009 <- comets[comets$ccf2009, ][-c(13:15), ]
> 
> # Sample size
> nrow(comets_ccf2009)
[1] 208
> 
> # Tests for the data in Cuesta-Albertos et al. (2009)
> tests_ccf2009 <- unif_test(data = comets_ccf2009$normal, type = type_tests,
+                            p_value = "asymp")
Series truncated from 10000 to 10000 terms (difference <= 0 with the HBE tail probability; last weight = 6.249e-14).
Error in is.finite(x) : default method not implemented for type 'list'
Calls: unif_test ... do.call -> p_sph_stat_PCvM -> cbind -> p_Sobolev -> p_wschisq
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘sphunif.Rmd’ using rmarkdown
Quitting from lines 39-41 (sphunif.Rmd) 
Error: processing vignette 'sphunif.Rmd' failed with diagnostics:
Not compatible with requested type: [type=list; target=double].
--- failed re-building ‘sphunif.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘gplots’
  All declared Imports should be used.
Found the following files/directories:
  ‘AlphaGA_3.txt’ ‘AlphaML_3.txt’ ‘BetaGA_3.txt’ ‘BetaML_3.txt’
  ‘Performance_GA_ML_ 3 .pdf’ ‘SPIGA_3Pmon.Pm_St1.pdf’
  ‘SPIGA_3Pmon.Pm_St2.pdf’ ‘SPI_AG_3.txt’ ‘SPI_ML_3.txt’
  ‘SPI_ML_3Pm_St1.pdf’ ‘SPI_ML_3Pm_St2.pdf’ ‘SPI_ML_3Pm_St3.pdf’
  ‘SPI_ML_3Pm_St4.pdf’ ‘SPI_PARAM_3.txt’ ‘SPI_PARAM_3Pm_St1.pdf’
  ‘SPI_PARAM_3Pm_St2.pdf’ ‘SPI_PARAM_3Pm_St3.pdf’
  ‘SPI_PARAM_3Pm_St4.pdf’
Packages in Depends field not imported from:
  ‘lars’ ‘parallel’ ‘randomForest’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘spikeslab/libs/spikeslab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'library' or 'require' call to ‘quadprog’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘quadprog’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPIn: no visible global function definition for ‘density’
SPIn: no visible global function definition for ‘quantile’
SPIn: no visible global function definition for ‘solve.QP’
bootSPIn: no visible global function definition for ‘runif’
plot.SPIn: no visible global function definition for ‘hist’
plot.SPIn: no visible global function definition for ‘lines’
plot.SPIn: no visible global function definition for ‘text’
plot.SPIn: no visible global function definition for ‘quantile’
plot.SPIn: no visible global function definition for ‘legend’
Undefined global functions or variables:
  density hist legend lines quantile runif solve.QP text
Consider adding
  importFrom("graphics", "hist", "legend", "lines", "text")
  importFrom("stats", "density", "quantile", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Running examples in ‘splinetree-Ex.R’ failed
The error most likely occurred in:

> ### Name: splineTree
> ### Title: Build a splinetree model.
> ### Aliases: splineTree
> 
> ### ** Examples
> 
> nlsySample_subset <- nlsySample[nlsySample$ID %in% sample(unique(nlsySample$ID), 500),]
> splitForm <- ~HISP+WHITE+BLACK+HGC_MOTHER+HGC_FATHER+SEX+Num_sibs
> tree1 <- splineTree(splitForm, BMI~AGE, 'ID', nlsySample_subset, degree=3, intercept=TRUE, cp=0.005)
Error in rpart(form, data = flat_data, method = ulist, control = control,  : 
  User 'eval' function returned invalid label
Calls: splineTree -> rpart
Execution halted
Running ‘testthat.R’ [11s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(splinetree)
  Loading required package: rpart
  Loading required package: nlme
  Loading required package: splines
  > 
  > test_check("splinetree")
  [1] "Building Tree:"
  [1] 1
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-tree.R:9:3): Testing Trees ──────────────────────────────────────
  Error in `rpart(form, data = flat_data, method = ulist, control = control, 
      parms = list(basisMatrix))`: User 'eval' function returned invalid label
  Backtrace:
      █
   1. └─splinetree::splineTree(...) test-tree.R:9:2
   2.   └─rpart::rpart(...)
  ── Error (test_forest.R:8:3): Building Forests ─────────────────────────────────
  Error in `rpart(form, data = sample, method = ulist, control = control, 
      maxcompete = 0, parms = list(basisMatrix, prob))`: User 'eval' function returned invalid label
  Backtrace:
      █
   1. └─splinetree::splineForest(...) test_forest.R:8:2
   2.   └─rpart::rpart(...)
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 2 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RSpectra’ ‘ggplot2’ ‘latex2exp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘reshape2’, ‘sampling’, ‘dplyr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘psy’ ‘ranger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘biomod2’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   4.1Mb
    libs      7.0Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
R2.global: no visible global function definition for ‘var’
calculer.var.exp: no visible global function definition for ‘var’
creer.noeud: no visible global function definition for ‘var’
ponderer.classe: no visible global function definition for ‘var’
ponderer.classe: no visible global function definition for ‘cov’
spodt: no visible global function definition for ‘model.frame’
spodt.tree: no visible global function definition for ‘plot.new’
spodt.tree: no visible global function definition for ‘par’
spodt.tree: no visible global function definition for ‘plot.window’
spodt.tree: no visible global function definition for ‘text’
spodt.tree: no visible global function definition for ‘segments’
test.spodt: no visible global function definition for ‘model.frame’
test.spodt: no visible global function definition for ‘hist’
test.spodt: no visible global function definition for ‘abline’
tracer.noeud: no visible global function definition for ‘text’
tracer.noeud: no visible global function definition for ‘segments’
Undefined global functions or variables:
  abline cov hist model.frame par plot.new plot.window segments text
  var
Consider adding
  importFrom("graphics", "abline", "hist", "par", "plot.new",
             "plot.window", "segments", "text")
  importFrom("stats", "cov", "model.frame", "var")
to your NAMESPACE file.
File ‘SPODT/libs/SPODT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 7587 marked UTF-8 strings
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.
fetch_NBAPlayerStatistics: no visible global function definition for
  ‘read.table’
Undefined global functions or variables:
  read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
Note: found 8 marked Latin-1 strings
  Note: found 83 marked UTF-8 strings
Namespace in Imports field not imported from: ‘batchtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggridges’
  All declared Imports should be used.
Running examples in ‘SPOT-Ex.R’ failed
The error most likely occurred in:

> ### Name: buildRSM
> ### Title: Build Response Surface Model
> ### Aliases: buildRSM
> 
> ### ** Examples
> 
> ## Create a test function: branin
> braninFunction <- function (x) {	
+ 	(x[2]  - 5.1/(4 * pi^2) * (x[1] ^2) + 5/pi * x[1]  - 6)^2 + 
+ 10 * (1 - 1/(8 * pi)) * cos(x[1] ) + 10
+ }
> ## Create design points
> x <- cbind(runif(20)*15-5,runif(20)*15)
> ## Compute observations at design points
> y <- as.matrix(apply(x,1,braninFunction))
> ## Create model with default settings
> fit <- buildRSM(x,y)
> ## Predict new point
> predict(fit,cbind(1,2))
$y
         [,1]
[1,] 37.13114

> ## True value at location
> braninFunction(c(1,2))
[1] 21.62764
> ## plots
> plot(fit)
> ## path of steepest descent
> descentSpotRSM(fit)
Path of steepest descent from ridge analysis:
Error: node stack overflow
Execution halted
Namespace in Imports field not imported from: ‘sampling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running examples in ‘spray-Ex.R’ failed
The error most likely occurred in:

> ### Name: knight
> ### Title: Generating function for a chess knight and king
> ### Aliases: knight king chess_knight
> 
> ### ** Examples
> 
> 
> ## How many ways can a knight return to its starting square in 6 moves?
> constant(knight()^6)
          val
 0 0  =  5840
> 
> ## How many in 6 or fewer?
> constant((1+knight())^6)
          val
 0 0  =  8481
> 
> ## Where does a randomly-moving knight end up?
> d <- xyz(2)
> kt <- (1+knight())*d^2/9
> persp(1:25,1:25,as.array(d*kt^6))
> 
> 
> ## what is the probability that a 4D king is a knight's move from
> ##   (0,0,0,0) after 6 moves?
> 
> sum(coeffs(((king(4)/80)^4)[knight(4)]))
Error in is_valid_spray(L) : is.matrix(L[[1]]) is not TRUE
Calls: coeffs ... spraymaker -> stopifnot -> is_valid_spray -> stopifnot
Execution halted
Running ‘testthat.R’ [14s/24s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > 
  > test_check("spray")
  Loading required package: spray
  
  Attaching package: 'spray'
  
  The following objects are masked from 'package:base':
  
      pmax, pmin
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_aaa.R:24:5): test suite aaa ─────────────────────────────────────
  <Rcpp::not_compatible/C++Error/error/condition>
  Error in `spray_maker(M, x)`: Not compatible with requested type: [type=list; target=integer].
  Backtrace:
       █
    1. ├─testthat::expect_silent(spray(spray(1:4), 3)) test_aaa.R:24:4
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat:::.capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. └─spray::spray(spray(1:4), 3)
   10.   └─spray::spraymaker(list(M, x), addrepeats = addrepeats)
   11.     └─spray::spray_maker(M, x)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 134 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘ggplot2’
  All declared Imports should be used.
Running examples in ‘sprm-Ex.R’ failed
The error most likely occurred in:

> ### Name: predict.prm
> ### Title: Predict method for models of class prm
> ### Aliases: predict.prm
> 
> ### ** Examples
> 
> set.seed(5023)
> U <- c(rep(2,20), rep(5,30))
> X <- replicate(6, U+rnorm(50))
> beta <- c(rep(1, 3), rep(-1,3))
> e <- c(rnorm(45,0,1.5),rnorm(5,-20,1))
> y <- X%*%beta + e
> d <- as.data.frame(X)
> d$y <- y
> mod <- prms(y~., data=d, a=2, fun="Hampel")
> 
> dnew <- as.data.frame(replicate(6, U+rnorm(10)))
> ynewp <- predict(mod, newdata=dnew)
Error in as.matrix(Xn) %*% b : non-conformable arguments
Calls: predict -> predict.prm
Execution halted
Rd file 'SlrArd.Rd':
  \usage lines wider than 90 characters:
     SlrArd(T, X, bias = TRUE, method = c("VB", "VBMacKay", "PX-VB"), control = list(), check.lb=TRUE, a0 = 0, b0 = 0, mu0 = 0, xi0 = 1)

These lines will be truncated in the PDF manual.
plot.SPRT: no visible global function definition for ‘par’
plot.SPRT: no visible global function definition for ‘abline’
print.SPRT: no visible global function definition for ‘head’
Undefined global functions or variables:
  abline head par
Consider adding
  importFrom("graphics", "abline", "par")
  importFrom("utils", "head")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘car’ ‘knitr’ ‘lmtest’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is 43.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  41.3Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Undeclared package ‘shiny’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘spatstat’ ‘spatstat.data’ ‘spatstat.linnet’ ‘spatstat.sparse’
  ‘spatstat.utils’ ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
sGda : <anonymous>: no visible global function definition for ‘cov’
sortgene: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  cov model.matrix
Consider adding
  importFrom("stats", "cov", "model.matrix")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘RSQLite’ ‘dbplyr’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'library' or 'require' calls in package code:
  ‘RJDBC’ ‘RMySQL’ ‘RODBC’ ‘RPostgreSQL’ ‘RSQLite’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
cacheQuery: no visible global function definition for ‘read.csv’
cacheQuery: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  read.csv write.csv
Consider adding
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
SQN: no visible binding for global variable ‘median’
SQN: no visible global function definition for ‘quantile’
SQN.demo.data: no visible global function definition for ‘rnorm’
mix.qn: no visible global function definition for ‘ecdf’
mix.qn: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  ecdf median quantile rnorm
Consider adding
  importFrom("stats", "ecdf", "median", "quantile", "rnorm")
to your NAMESPACE file.
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    libs  22.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘RColorBrewer’, ‘colorspace’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared package ‘plyr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shinyFiles’
  All declared Imports should be used.
ssd : correction_method_D: no visible global function definition for
  ‘rnorm’
ssd : generate_bootstrap: no visible global function definition for
  ‘rmultinom’
ssd : bootstrap_method: no visible global function definition for
  ‘median’
ssd : bootstrap_method: no visible global function definition for
  ‘quantile’
ssd : unbalanced_generate_bootstrap: no visible global function
  definition for ‘rmultinom’
ssd : unbalanced_bootstrap_method: no visible global function
  definition for ‘median’
ssd : unbalanced_bootstrap_method: no visible global function
  definition for ‘quantile’
ssd: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  median qchisq quantile rmultinom rnorm
Consider adding
  importFrom("stats", "median", "qchisq", "quantile", "rmultinom",
             "rnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
L_hNV: no visible global function definition for ‘pnorm’
L_hNV_rho: no visible global function definition for ‘pnorm’
eff.ssfa: no visible global function definition for ‘pnorm’
plot_fitted: no visible global function definition for ‘lines’
plot_moran: no visible global function definition for ‘residuals’
print.summary.ssfa: no visible global function definition for
  ‘printCoefmat’
ssfa: no visible global function definition for ‘model.frame’
ssfa: no visible global function definition for ‘model.response’
ssfa.fit: no visible global function definition for ‘lm’
ssfa.fit: no visible global function definition for ‘var’
ssfa.fit: no visible global function definition for ‘logLik’
summary.ssfa: no visible global function definition for ‘pnorm’
summary.ssfa: no visible global function definition for ‘logLik’
summary.ssfa: no visible global function definition for ‘pchisq’
summary.ssfa: no visible binding for global variable ‘df’
u.ssfa: no visible global function definition for ‘dnorm’
u.ssfa: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  df dnorm lines lm logLik model.frame model.response pchisq pnorm
  printCoefmat residuals var
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "df", "dnorm", "lm", "logLik", "model.frame",
             "model.response", "pchisq", "pnorm", "printCoefmat",
             "residuals", "var")
to your NAMESPACE file.
Package in Depends field not imported from: ‘survey’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fit.model: no visible global function definition for ‘hadamard’
Undefined global functions or variables:
  hadamard
Malformed Title field: should not end in a period.
mem.usage: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  read.delim
Consider adding
  importFrom("utils", "read.delim")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
installed size is 70.8Mb
  sub-directories of 1Mb or more:
    libs  70.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Running examples in ‘SSM-Ex.R’ failed
The error most likely occurred in:

> ### Name: likelihood.plot
> ### Title: Plot the concentrated likelihood of an SSM.
> ### Aliases: likelihood.plot
> 
> ### ** Examples
> 
> data(attitude)
> X <- transform11(attitude[ 2:7])
> Y <- attitude[ , 1]
> s <- fit.ssm(X, Y, GP = TRUE)
Error in fit.ssm(X, Y, GP = TRUE) : 
  There are not the same number of responses as design points.
Execution halted
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
map.world: no visible global function definition for ‘par’
map.world: no visible global function definition for ‘plot.new’
map.world: no visible global function definition for ‘plot.window’
map.world: no visible global function definition for ‘lines’
map.world: no visible global function definition for ‘title’
map.world: no visible global function definition for ‘axis’
map.world: no visible global function definition for ‘box’
plot.smooth.sspline: no visible global function definition for
  ‘predict’
plot.smooth.sspline: no visible global function definition for
  ‘filled.contour’
plot.smooth.sspline: no visible binding for global variable
  ‘terrain.colors’
plot.smooth.sspline: no visible global function definition for ‘title’
plot.smooth.sspline: no visible global function definition for ‘axis’
station: no visible binding for global variable ‘WTdiff’
station: no visible global function definition for ‘points’
Undefined global functions or variables:
  WTdiff axis box filled.contour lines par plot.new plot.window points
  predict terrain.colors title
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "axis", "box", "filled.contour", "lines", "par",
             "plot.new", "plot.window", "points", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
File ‘sspline/libs/sspline.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘scanstatistics’
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
Undeclared package ‘XML’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shinydashboard’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
error.est : <anonymous>: no visible global function definition for
  ‘median’
holm.robust: no visible global function definition for ‘pnorm’
holm.robust: no visible global function definition for ‘median’
holm.robust: no visible global function definition for ‘mad’
huberize: no visible global function definition for ‘quantile’
ssvd.initial: no visible global function definition for ‘mad’
ssvd.iter.thresh: no visible global function definition for ‘mad’
Undefined global functions or variables:
  mad median pnorm quantile
Consider adding
  importFrom("stats", "mad", "median", "pnorm", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 123 marked UTF-8 strings
Namespace in Imports field not imported from: ‘stabledist’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘mice’ ‘sandwich’ ‘zoo’
  All declared Imports should be used.
Undeclared packages ‘pryr’, ‘functional’, ‘dplyr’, ‘ks’, ‘purrr’, ‘data.table’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘workflowsets’ ‘yardstick’
  All declared Imports should be used.
Undeclared packages ‘h2o’, ‘SuperLearner’ in Rd xrefs
Note: found 40659 marked UTF-8 strings
genericPlot: no visible global function definition for ‘dev.new’
genericPlot: no visible global function definition for ‘par’
genericPlot: no visible global function definition for ‘rainbow’
genericPlot: no visible global function definition for ‘lines’
genericPlot: no visible global function definition for ‘legend’
genericPlot: no visible global function definition for ‘dev.copy2pdf’
genericPlot: no visible global function definition for ‘dev.copy2eps’
genericPlot: no visible global function definition for ‘dev.print’
genericPlot: no visible binding for global variable ‘png’
genericPlot: no visible binding for global variable ‘tiff’
plotStrains: no visible global function definition for ‘rainbow’
plotStrains: no visible global function definition for ‘dev.new’
plotStrains: no visible global function definition for ‘par’
plotStrains: no visible global function definition for ‘lines’
plotStrains: no visible global function definition for ‘legend’
plotStrains: no visible global function definition for ‘dev.copy2pdf’
plotStrains: no visible global function definition for ‘dev.copy2eps’
plotStrains: no visible global function definition for ‘dev.print’
plotStrains: no visible binding for global variable ‘png’
plotStrains: no visible binding for global variable ‘tiff’
Undefined global functions or variables:
  dev.copy2eps dev.copy2pdf dev.new dev.print legend lines par png
  rainbow tiff
Consider adding
  importFrom("grDevices", "dev.copy2eps", "dev.copy2pdf", "dev.new",
             "dev.print", "png", "rainbow", "tiff")
  importFrom("graphics", "legend", "lines", "par")
to your NAMESPACE file.
Found the following files/directories:
  ‘Rplot001.pdf’
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  25.0Mb
Namespaces in Imports field not imported from:
  ‘reshape2’ ‘stats’
  All declared Imports should be used.
Non-standard file/directory found at top level:
  ‘Licence’
'library' or 'require' calls to packages already attached by Depends:
  ‘np’ ‘sp’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘np’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
stkde: no visible global function definition for ‘npudensbw’
stkde: no visible global function definition for ‘npudens’
stkde: no visible global function definition for ‘quantile’
stkde: no visible global function definition for ‘heat.colors’
stkde: no visible global function definition for ‘par’
stkde: no visible global function definition for ‘image’
stkde: no visible global function definition for ‘contour’
stkde.base: no visible global function definition for ‘npudensbw’
stkde.base: no visible global function definition for ‘npudens’
stkde.sig: no visible global function definition for ‘SpatialPoints’
stkde.sig: no visible global function definition for ‘spsample’
stkde.sig: no visible global function definition for ‘bbox’
stkde.sig: no visible global function definition for ‘quantile’
stkde.sig: no visible global function definition for ‘heat.colors’
stkde.sig: no visible global function definition for ‘par’
stkde.sig: no visible global function definition for ‘image’
stkde.sig: no visible global function definition for ‘contour’
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.
Rd file 'stkde.sig.rd':
  \examples lines wider than 100 characters:
     system.time(stkde.sig(d[,1],d[,2],d[,3],xgrids=20,ygrids=20,breaks=0.05,sim=3,alpha=0.05,nrowspar=1))
     #determines how much real and CPU time (in seconds) the currently running R process has already taken
     system.time(stkde.sig(d[,1],d[,2],d[,3],xgrids=20,ygrids=20,breaks=0.05,sim=3,alpha=0.05,nrowspar=2))
     #determines how much real and CPU time (in seconds) the currently running R process has already taken

These lines will be truncated in the PDF manual.
installed size is 43.2Mb
  sub-directories of 1Mb or more:
    libs  42.9Mb
find.names: no visible global function definition for ‘na.omit’
generate.names: no visible global function definition for ‘na.omit’
standardize.countrynames: no visible global function definition for
  ‘data’
standardize.names: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
Rd file 'standardize.countrynames.Rd':
  \usage lines wider than 90 characters:
     standardize.countrynames(input, input.column = NULL, standard = "default", standard.column = NULL, only.names = FALSE, na.rm = FALSE, s ... [TRUNCATED]

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

These lines will be truncated in the PDF manual.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
installed size is 193.2Mb
  sub-directories of 1Mb or more:
    lib    27.7Mb
    libs  163.8Mb
Undeclared packages ‘rstan’, ‘rstanarm’ in Rd xrefs
GNU make is a SystemRequirements.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    include  10.7Mb
    lib       3.0Mb
installed size is 70.9Mb
  sub-directories of 1Mb or more:
    libs  70.1Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘latex2exp’ ‘rstantools’ ‘tidyverse’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘iterators’ ‘methods’ ‘rgdal’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘mnlogit’
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.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘codetools’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘codetools’ ‘gss’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘STAR/libs/STAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘pander’ ‘readr’ ‘tidyselect’
  All declared Imports should be used.
Package suggested but not available for checking: ‘starsdata’
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc   2.3Mb
    nc    4.5Mb
'LazyData' is specified without a 'data' directory
Note: found 14 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘rgr’ in Rd xrefs
Running examples in ‘StatDA-Ex.R’ failed
The error most likely occurred in:

> ### Name: plotmvoutlier
> ### Title: Multivariate outlier plot
> ### Aliases: plotmvoutlier
> ### Keywords: multivariate dplot
> 
> ### ** Examples
> 
> data(moss)
> X=moss[,"XCOO"]
> Y=moss[,"YCOO"]
> el=c("Ag","As","Bi","Cd","Co","Cu","Ni")
> x=log10(moss[,el])
> 
> data(kola.background)
> plotmvoutlier(cbind(X,Y),x,symb=FALSE,map.col=c("grey","grey","grey","grey"),
+        map.lwd=c(1,1,1,1),
+        xlab="",ylab="",frame.plot=FALSE,xaxt="n",yaxt="n")
Error in FUN(x, aperm(array(STATS, dims[perm]), order(perm)), ...) : 
  non-numeric argument to binary operator
Calls: plotmvoutlier -> mahalanobis -> sweep
Execution halted
Found the following files/directories:
  ‘testmat.sdml’ ‘testmat2.sdml’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   4.5Mb
Package suggested but not available for checking: ‘asreml’
Running ‘testthat.R’ [44s/55s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(statgenGxE)
  > 
  > test_check("statgenGxE")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (16)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-multMissing.R:20:3): multMissing preserves input class ──────────
  Error in `multMissing(D)`: 'list' object cannot be coerced to type 'double'
  Backtrace:
      █
   1. ├─testthat::expect_is(multMissing(D), "data.frame") test-multMissing.R:20:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─statgenGxE::multMissing(D)
  ── Error (test-multMissing.R:34:3): multMissing imputes correct values ─────────
  Error in `multMissing(D)`: 'list' object cannot be coerced to type 'double'
  Backtrace:
      █
   1. ├─testthat::expect_equal(...) test-multMissing.R:34:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─statgenGxE::multMissing(D)
  ── Error (test-multMissing.R:41:3): option maxIter functions properly ──────────
  Error in `multMissing(D, maxIter = 1)`: 'list' object cannot be coerced to type 'double'
  Backtrace:
      █
   1. ├─testthat::expect_warning(...) test-multMissing.R:41:2
   2. │ └─testthat:::quasi_capture(enquo(object), label, capture_warnings)
   3. │   ├─testthat:::.capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─statgenGxE::multMissing(D, maxIter = 1)
  
  [ FAIL 3 | WARN 37 | SKIP 16 | PASS 437 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘distrEx’ in Rd xrefs
'LazyData' is specified without a 'data' directory
actvspred: no visible global function definition for ‘quantile’
actvspred: no visible global function definition for ‘aggregate’
actvspred: no visible global function definition for ‘par’
actvspred: no visible global function definition for ‘lines’
auc: no visible global function definition for ‘par’
decile: no visible global function definition for ‘quantile’
dqcontinuous : numoutliers: no visible global function definition for
  ‘quantile’
dqcontinuous : <anonymous>: no visible global function definition for
  ‘sd’
dqcontinuous : <anonymous>: no visible global function definition for
  ‘quantile’
gini: no visible global function definition for ‘par’
gini: no visible global function definition for ‘abline’
iv: no visible global function definition for ‘quantile’
iv: no visible global function definition for ‘aggregate’
ks: no visible global function definition for ‘aggregate’
ks: no visible global function definition for ‘par’
ks: no visible global function definition for ‘lines’
outliers: no visible global function definition for ‘quantile’
outliers: no visible global function definition for ‘na.omit’
pentile: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline aggregate lines na.omit par quantile sd
Consider adding
  importFrom("graphics", "abline", "lines", "par")
  importFrom("stats", "aggregate", "na.omit", "quantile", "sd")
to your NAMESPACE file.
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
Note: found 52 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mathjaxr’
  All declared Imports should be used.
Undeclared package ‘fortunes’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    shiny-apps   6.2Mb
Namespaces in Imports field not imported from:
  ‘DDoutlier’ ‘car’ ‘corrplot’ ‘data.table’ ‘energy’ ‘ggplot2’
  ‘gridExtra’ ‘kableExtra’ ‘knitr’ ‘readr’ ‘reshape2’ ‘rmarkdown’
  ‘shinydisconnect’
  All declared Imports should be used.
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘gbm’ ‘ggfortify’ ‘tibble’ ‘tidyverse’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
File ‘steadyICA/libs/steadyICA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
getStp: no visible global function definition for ‘lm’
plot.steeptest: no visible global function definition for ‘axis’
plot.steeptest: no visible global function definition for ‘box’
plot.steeptest: no visible global function definition for ‘lm’
plot.steeptest: no visible global function definition for ‘abline’
plot.steeptest: no visible global function definition for ‘legend’
plot.steeptest: no visible global function definition for
  ‘as.graphicsAnnot’
steeptest: no visible global function definition for ‘lm’
summary.steeptest: no visible global function definition for ‘var’
summary.steeptest: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline as.graphicsAnnot axis box legend lm quantile var
Consider adding
  importFrom("grDevices", "as.graphicsAnnot")
  importFrom("graphics", "abline", "axis", "box", "legend")
  importFrom("stats", "lm", "quantile", "var")
to your NAMESPACE file.
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.
'library' or 'require' call to ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
Stem.Bootstrap: no visible global function definition for ‘runif’
filtering: no visible global function definition for ‘is.ts’
filtering: no visible global function definition for ‘ts’
filtering: no visible global function definition for ‘start’
filtering: no visible global function definition for ‘end’
filtering: no visible global function definition for ‘frequency’
kalman: no visible global function definition for ‘ts’
smoothing: no visible global function definition for ‘is.ts’
smoothing: no visible global function definition for ‘ts’
smoothing: no visible global function definition for ‘start’
smoothing: no visible global function definition for ‘end’
smoothing: no visible global function definition for ‘frequency’
Undefined global functions or variables:
  end frequency is.ts runif start ts
Consider adding
  importFrom("stats", "end", "frequency", "is.ts", "runif", "start",
             "ts")
to your NAMESPACE file.
Error(s) in re-building vignettes:
--- re-building ‘STEPCAM.Rmd’ using rmarkdown
Quitting from lines 53-56 (STEPCAM.Rmd) 
Error: processing vignette 'STEPCAM.Rmd' failed with diagnostics:
length of 'dimnames' [1] not equal to array extent
--- failed re-building ‘STEPCAM.Rmd’

--- re-building ‘STEPCAM_plotting.Rmd’ using rmarkdown
Quitting from lines 18-26 (STEPCAM_plotting.Rmd) 
Error: processing vignette 'STEPCAM_plotting.Rmd' failed with diagnostics:
length of 'dimnames' [1] not equal to array extent
--- failed re-building ‘STEPCAM_plotting.Rmd’

SUMMARY: processing the following files failed:
  ‘STEPCAM.Rmd’ ‘STEPCAM_plotting.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
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.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
Found the following files/directories:
  ‘corrviz.html’
Namespaces in Imports field not imported from:
  ‘huge’ ‘readr’ ‘scales’ ‘shinyjs’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.7Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
Rd file 'calc.stoich.coef.Rd':
  \usage lines wider than 90 characters:
     calc.stoich.coef(alpha, name, subst, subst.norm, nu.norm = 1, constraints = list(), eps = 1e-5, verbose = TRUE)

These lines will be truncated in the PDF manual.
Note: found 22806 marked UTF-8 strings
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Note: found 1 marked UTF-8 string
Running ‘testthat.R’ [44s/59s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(strand)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("strand")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_normalize.R:96:3): adj_var with one variable ────────────────────
  Error in `normalize(df, in_var = "x", adj_var = "w")`: is.null(in_var) && is.null(within_var) && is.null(adj_var) is not TRUE
  Backtrace:
      █
   1. └─strand:::normalize(df, in_var = "x", adj_var = "w") test_normalize.R:96:2
   2.   └─base::stopifnot(is.null(in_var) && is.null(within_var) && is.null(adj_var))
  ── Error (test_normalize.R:121:1): (code run outside of `test_that()`) ─────────
  Error in `normalize(data.frame(x = c(10, 1, 100)), in_var = "x")`: is.null(in_var) && is.null(within_var) && is.null(adj_var) is not TRUE
  Backtrace:
      █
   1. ├─testthat::expect_equal(...) test_normalize.R:121:0
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─strand:::normalize(data.frame(x = c(10, 1, 100)), in_var = "x")
   5.   └─base::stopifnot(is.null(in_var) && is.null(within_var) && is.null(adj_var))
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 74 ]
  Error: Test failures
  Execution halted
StratPhyloCongruence: no visible global function definition for ‘runif’
StratPhyloCongruence: no visible global function definition for
  ‘txtProgressBar’
StratPhyloCongruence: no visible global function definition for
  ‘setTxtProgressBar’
StratPhyloCongruence: no visible global function definition for ‘pnorm’
StratPhyloCongruence: no visible global function definition for ‘sd’
geoscalePhylo: no visible global function definition for ‘data’
geoscalePhylo: no visible global function definition for ‘par’
geoscalePhylo: no visible global function definition for ‘text’
geoscalePhylo: no visible global function definition for ‘segments’
geoscalePhylo: no visible global function definition for ‘rect’
geoscalePhylo: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  data par pnorm rect rgb runif sd segments setTxtProgressBar text
  txtProgressBar
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "par", "rect", "segments", "text")
  importFrom("stats", "pnorm", "runif", "sd")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Running examples in ‘stratamatch-Ex.R’ failed
The error most likely occurred in:

> ### Name: strata_match
> ### Title: Strata Match
> ### Aliases: strata_match
> 
> ### ** Examples
> 
> # make a sample data set
> set.seed(1)
> dat <- make_sample_data(n = 75)
> 
> # stratify with auto_stratify
> a.strat <- auto_stratify(dat, "treat", outcome ~ X2, size = 25)
Constructing a pilot set by subsampling 10% of controls.
Fitting prognostic model via logistic regression: outcome ~ X2
> 
> # 1:1 match based on propensity formula: treat ~ X1 + X2
> strata_match(a.strat, model = treat ~ X1 + X2, k = 1)
This function makes essential use of the optmatch package, which has an academic license.
For more information, run optmatch::relaxinfo()
Fitting propensity model: treat ~ X1 + X2

Error in fullmatch.BlockedInfinitySparseMatrix(x = x, min.controls = controls,  : 
  Some elements of the distance matrix are not found in the data argument.
Calls: strata_match ... pairmatch.BlockedInfinitySparseMatrix -> fullmatch -> fullmatch.BlockedInfinitySparseMatrix
Execution halted
Running ‘testthat.R’ [10s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(stratamatch)
  > 
  > test_check("stratamatch")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-match_functions.R:18:3): matching works ─────────────────────────
  Error in `fullmatch.BlockedInfinitySparseMatrix(x = x, min.controls = controls, 
      max.controls = controls, omit.fraction = omf, data = data, 
      ...)`: Some elements of the distance matrix are not found in the data argument.
  Backtrace:
      █
   1. └─stratamatch::strata_match(m.strat, treated ~ X1, k = 1) test-match_functions.R:18:2
   2.   ├─optmatch::pairmatch(matchdist, data = object$analysis_set, controls = k)
   3.   └─optmatch:::pairmatch.BlockedInfinitySparseMatrix(...)
   4.     ├─optmatch::fullmatch(...)
   5.     └─optmatch:::fullmatch.BlockedInfinitySparseMatrix(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 278 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Advanced_functionality.Rmd’ using rmarkdown
Quitting from lines 185-189 (Advanced_functionality.Rmd) 
Error: processing vignette 'Advanced_functionality.Rmd' failed with diagnostics:
Some elements of the distance matrix are not found in the data argument.
--- failed re-building ‘Advanced_functionality.Rmd’

--- re-building ‘Intro_to_stratamatch.Rmd’ using rmarkdown
Quitting from lines 261-266 (Intro_to_stratamatch.Rmd) 
Error: processing vignette 'Intro_to_stratamatch.Rmd' failed with diagnostics:
Some elements of the distance matrix are not found in the data argument.
--- failed re-building ‘Intro_to_stratamatch.Rmd’

SUMMARY: processing the following files failed:
  ‘Advanced_functionality.Rmd’ ‘Intro_to_stratamatch.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
Found the following files/directories:
  ‘myNewStrat.R’
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Package suggested but not available for checking: ‘StrathE2E2examples’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘bnlearn’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
File ‘strat/libs/strat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ks’
  All declared Imports should be used.
Undeclared package ‘HDoutliers’ in Rd xrefs
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   9.4Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘STRaitRazoR’
Namespaces in Imports field not imported from:
  ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
  All declared Imports should be used.
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
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.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘pls’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘glue’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘UpSetR’ ‘alluvial’ ‘gridBase’
  All declared Imports should be used.
identifyGraph: no visible global function definition for ‘phyper’
mytriangle: no visible global function definition for ‘symbols’
plotGraph: no visible global function definition for ‘par’
updateOrgEnvir: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  par phyper read.table symbols
Consider adding
  importFrom("graphics", "par", "symbols")
  importFrom("stats", "phyper")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘bsplus’ ‘colourpicker’ ‘grDevices’ ‘graphics’ ‘jsonlite’
  ‘purrr’ ‘shinyWidgets’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'library' or 'require' calls to packages already attached by Depends:
  ‘ROCR’ ‘penalized’
  Please remove these calls from your code.
ELF: no visible global function definition for ‘pt’
ELF: no visible global function definition for ‘qnorm’
ELF: no visible global function definition for ‘lm’
ELF: no visible global function definition for ‘lowess’
ELF: no visible global function definition for ‘dnorm’
ELF: no visible global function definition for ‘approx’
subtype: no visible global function definition for ‘runif’
subtype: no visible global function definition for ‘hclust’
subtype: no visible global function definition for ‘dist’
subtype: no visible global function definition for ‘cutree’
subtype: no visible global function definition for ‘pt’
subtype: no visible global function definition for ‘heatmap’
test_subtype_only: no visible global function definition for ‘pt’
test_subtype_only: no visible global function definition for ‘survdiff’
test_subtype_only: no visible global function definition for ‘survfit’
test_subtype_only: no visible global function definition for ‘title’
ufun: no visible global function definition for ‘dnorm’
ufun: no visible global function definition for ‘lowess’
Undefined global functions or variables:
  approx cutree dist dnorm hclust heatmap lm lowess pt qnorm runif
  survdiff survfit title
Consider adding
  importFrom("graphics", "title")
  importFrom("stats", "approx", "cutree", "dist", "dnorm", "hclust",
             "heatmap", "lm", "lowess", "pt", "qnorm", "runif")
to your NAMESPACE file.
Rd file 'subtype.Rd':
  \usage lines wider than 90 characters:
     subtype(GEset, outcomeLabels, treatment=NULL, Npermutes=10, Nchunks = 25, minClusterSizeB = 20, NclustersASet = 100, FDRpermutation = T ... [TRUNCATED]
  \examples lines wider than 100 characters:
     summary(A,f.out=0)  ### f.out can be used for filtering out uninteresting subtypes. e.g. if f.out=2, we ignore subtypes having N01_0<=2 ... [TRUNCATED]

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

These lines will be truncated in the PDF manual.
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘tkrplot’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
playSudoku : replot: no visible global function definition for ‘par’
playSudoku : replot: no visible global function definition for
  ‘segments’
playSudoku : replot: no visible global function definition for ‘text’
playSudoku: no visible global function definition for ‘tktoplevel’
playSudoku: no visible global function definition for ‘tkwm.title’
playSudoku: no visible global function definition for ‘tkrplot’
playSudoku: no visible global function definition for ‘tktext’
playSudoku: no visible global function definition for ‘tkscrollbar’
playSudoku : <anonymous>: no visible global function definition for
  ‘tkyview’
playSudoku: no visible global function definition for ‘tkconfigure’
playSudoku : <anonymous>: no visible global function definition for
  ‘tkset’
playSudoku: no visible global function definition for ‘tkpack’
playSudoku: no visible global function definition for ‘tcl’
playSudoku: no visible global function definition for ‘tkcget’
playSudoku : showz: no visible global function definition for
  ‘tkrreplot’
playSudoku : type: no visible global function definition for ‘tkinsert’
playSudoku : type: no visible global function definition for ‘tksee’
playSudoku : kb: no visible global function definition for ‘tkdestroy’
playSudoku: no visible global function definition for
  ‘getGraphicsEvent’
playSudoku: no visible global function definition for ‘tkbind’
playSudoku: no visible global function definition for ‘tkwait.window’
Undefined global functions or variables:
  getGraphicsEvent par segments tcl text tkbind tkcget tkconfigure
  tkdestroy tkinsert tkpack tkrplot tkrreplot tkscrollbar tksee tkset
  tktext tktoplevel tkwait.window tkwm.title tkyview
Consider adding
  importFrom("grDevices", "getGraphicsEvent")
  importFrom("graphics", "par", "segments", "text")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
SUE.fitted.values: no visible global function definition for
  ‘model.frame’
SUE.lm: no visible global function definition for ‘model.frame’
SUE.lm: no visible global function definition for ‘lm’
SUE.lm: no visible global function definition for ‘anova’
SUE.residuals: no visible global function definition for ‘model.frame’
parameters : para2: no visible global function definition for ‘uniroot’
parameters: no visible global function definition for ‘optimize’
parameters: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  anova lm model.frame optimize uniroot
Consider adding
  importFrom("stats", "anova", "lm", "model.frame", "optimize",
             "uniroot")
to your NAMESPACE file.
Rd file 'SUE.lm.Rd':
  \examples lines wider than 100 characters:
     ##We analysis the well known stackloss data by using ordinary linear method and the subsampling method. 
     ##proportion of outliers in the data. The subsample size is chosen to be the default size of ns = 11.
     plot(SUE.fitted.values(a2),SUE.residuals(a2),xlab="(b) fitted values",ylab="residuals",ylim=c(-12,12))
     plot(SUE.fitted.values(a3),SUE.residuals(a3),xlab="(c) fitted values",ylab="residuals",ylim=c(-12,12))

These lines will be truncated in the PDF manual.
Namespaces in Imports field not imported from:
  ‘lwgeom’ ‘utf8’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘SummaryLasso/libs/SummaryLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 78 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
MCMCCV: no visible global function definition for ‘rnorm’
MLCVGauss: no visible global function definition for ‘runif’
MLCVGauss: no visible global function definition for ‘optim’
SimSunderData: no visible global function definition for ‘runif’
SimSunderData: no visible global function definition for ‘dist’
SimSunderData: no visible global function definition for ‘rnorm’
SimSunderData: no visible global function definition for ‘qgamma’
SimSunderData: no visible global function definition for ‘pnorm’
SimSunderData: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  dist optim pnorm qgamma rmultinom rnorm runif
Consider adding
  importFrom("stats", "dist", "optim", "pnorm", "qgamma", "rmultinom",
             "rnorm", "runif")
to your NAMESPACE file.
File ‘Sunder/libs/Sunder.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
sunter: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
supcluster : itgamma: no visible global function definition for
  ‘rgamma’
supcluster : itgamma: no visible global function definition for
  ‘dgamma’
supcluster : itgamma: no visible global function definition for ‘runif’
supcluster : itbeta: no visible global function definition for ‘rnorm’
supcluster : itbeta: no visible global function definition for ‘runif’
supcluster : itj: no visible global function definition for ‘dmultinom’
supcluster: no visible global function definition for ‘kmeans’
tab1: no visible global function definition for ‘image’
tab1: no visible global function definition for ‘gray’
tab1: no visible global function definition for ‘var’
Undefined global functions or variables:
  dgamma dmultinom gray image kmeans rgamma rnorm runif var
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image")
  importFrom("stats", "dgamma", "dmultinom", "kmeans", "rgamma", "rnorm",
             "runif", "var")
to your NAMESPACE file.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    doc  12.2Mb
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
Running ‘testthat.R’ [72s/91s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("superb")
  Loading required package: superb
  ==> THIS IS A TEST OF runDebug <==
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_subsidiaryFunctions.R:13:5): Testing Welch degree of freedom ──
  WelchDegreeOfFreedom(dta, "DV.1", "grp") not equal to 1.8988764.
  1/1 mismatches
  [1] NaN - 1.9 == NaN
  ── Error (test_superbPlot.R:466:5): Testing pre and post processing ────────────
  Error in `sdp/sds * (t(Z) - colMeans(Z))`: non-conformable arrays
  Backtrace:
       █
    1. ├─testthat::expect_message(...) test_superbPlot.R:466:4
    2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)
    3. │   ├─testthat:::.capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─superb::superbPlot(...)
    7.   └─plyr::ddply(...)
    8.     └─plyr::ldply(...)
    9.       └─plyr::llply(...)
   10.         ├─plyr:::loop_apply(n, do.ply)
   11.         └─(function (i) ...
   12.           └─superb:::.fun(piece, ...)
  
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 161 ]
  Error: Test failures
  Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'LazyData' is specified without a 'data' directory
TrainSuperMDS: no visible global function definition for ‘rnorm’
TrainSuperMDSOnce: no visible global function definition for ‘cmdscale’
TrainSuperMDSOnce: no visible global function definition for ‘quantile’
distmat: no visible global function definition for ‘dist’
Undefined global functions or variables:
  cmdscale dist quantile rnorm
Consider adding
  importFrom("stats", "cmdscale", "dist", "quantile", "rnorm")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘backports’ ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R.matlab’ ‘fBasics’ ‘spls’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running examples in ‘supervisedPRIM-Ex.R’ failed
The error most likely occurred in:

> ### Name: predict.supervisedPRIM
> ### Title: Model Predictions
> ### Aliases: predict.supervisedPRIM
> 
> ### ** Examples
> 
> # Train a model to determine if a flower is setosa
> data(iris)
> yData <- factor(ifelse(iris$Species == "setosa", "setosa", "other"), levels = c("setosa", "other"))
> xData <- iris
> xData$Species <- NULL
> primModel <- supervisedPRIM(x = xData, y = yData)
Error in box.curr[1, j] : subscript out of bounds
Calls: supervisedPRIM -> prim.box -> prim.which.box
Execution halted
Undeclared package ‘mded’ in Rd xrefs
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘pROC’
  All declared Imports should be used.
Undeclared package ‘truncdist’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘learnr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

plot.survAUC: no visible global function definition for ‘lines’
plot.survErr: no visible global function definition for ‘lines’
schemper: no visible global function definition for ‘predict’
schemper: no visible global function definition for ‘survfit’
schemper: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx lines predict survfit
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
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.
'LazyData' is specified without a 'data' directory
pearson: no visible global function definition for ‘cor’
plot.survcorr: no visible global function definition for ‘pnorm’
plot.survcorr: no visible global function definition for ‘par’
plot.survcorr: no visible global function definition for ‘points’
survcorr: no visible global function definition for ‘model.frame’
survcorr: no visible global function definition for ‘qnorm’
survcorr: no visible global function definition for ‘runif’
survcorr: no visible global function definition for ‘pnorm’
survcorr: no visible global function definition for ‘var’
survcorr: no visible global function definition for ‘qt’
Undefined global functions or variables:
  cor model.frame par pnorm points qnorm qt runif var
Consider adding
  importFrom("graphics", "par", "points")
  importFrom("stats", "cor", "model.frame", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.4Mb
    libs   1.5Mb
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    libs  37.0Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
AER: no visible binding for global variable ‘survexp.fr’
AER: no visible global function definition for ‘na.omit’
AER: no visible global function definition for ‘survexp’
AER: no visible global function definition for ‘poisson’
AER: no visible global function definition for ‘glm’
AER: no visible global function definition for ‘qnorm’
LR: no visible binding for global variable ‘survexp.fr’
LR: no visible global function definition for ‘na.omit’
LR: no visible global function definition for ‘survexp’
LR: no visible global function definition for ‘pchisq’
SMR: no visible binding for global variable ‘survexp.fr’
SMR: no visible global function definition for ‘na.omit’
SMR: no visible global function definition for ‘survexp’
SMR: no visible global function definition for ‘qnorm’
SMR: no visible global function definition for ‘pchisq’
SMR: no visible global function definition for ‘glm’
SMR: no visible binding for global variable ‘poisson’
survexp_plot: no visible binding for global variable ‘survexp.fr’
survexp_plot: no visible global function definition for ‘na.omit’
survexp_plot: no visible global function definition for ‘par’
survexp_plot: no visible global function definition for ‘survfit’
survexp_plot: no visible global function definition for ‘survexp’
survexp_plot: no visible global function definition for ‘lines’
survexp_plot: no visible global function definition for ‘legend’
survexp_plot: no visible global function definition for ‘curve’
survexp_plot: no visible global function definition for ‘arrows’
survexp_plot: no visible global function definition for ‘points’
Undefined global functions or variables:
  arrows curve glm legend lines na.omit par pchisq points poisson qnorm
  survexp survexp.fr survfit
Consider adding
  importFrom("graphics", "arrows", "curve", "legend", "lines", "par",
             "points")
  importFrom("stats", "glm", "na.omit", "pchisq", "poisson", "qnorm")
to your NAMESPACE file.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘survival’ which was already attached by Depends.
  Please remove these calls from your code.
Survgini: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
installed size is 126.6Mb
  sub-directories of 1Mb or more:
    libs  125.7Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘survC1’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Est.HR.FUN: no visible global function definition for ‘coxph’
Est.HR.FUN: no visible global function definition for ‘basehaz’
Est.HR.FUN: no visible global function definition for ‘approx’
Ghat.FUN: no visible global function definition for ‘survfit’
IDI.INF: no visible global function definition for ‘kmcens’
IDI.INF: no visible global function definition for ‘quantile’
IDI.INF.GRAPH: no visible global function definition for ‘lines’
IDI.INF.GRAPH: no visible global function definition for ‘abline’
IDI.INF.GRAPH: no visible global function definition for ‘points’
IDI.INF.GRAPH: no visible global function definition for ‘title’
PTB.IDI.FUN: no visible global function definition for ‘rexp’
shade: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  abline approx basehaz coxph kmcens lines points polygon quantile rexp
  survfit title
Consider adding
  importFrom("graphics", "abline", "lines", "points", "polygon", "title")
  importFrom("stats", "approx", "quantile", "rexp")
to your NAMESPACE file.
Rd file 'IDI.INF.GRAPH.Rd':
  \usage lines wider than 90 characters:
     IDI.INF.GRAPH(x, main = NULL, xlab = NULL, ylab = NULL, cex.main = NULL, cex.lab = NULL, ...)

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘readr’ ‘rlang’ ‘survival’ ‘tidyverse’ ‘utils’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.9Mb
    doc    3.5Mb
Malformed Description field: should contain one or more complete sentences.
File ‘survivalROC/libs/survivalROC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Note: found 366 marked UTF-8 strings
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
Undeclared package ‘survJamda’ in Rd xrefs
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   6.6Mb
Malformed Description field: should contain one or more complete sentences.
dlgMessage.tcltkGUI: no visible global function definition for ‘alarm’
Undefined global functions or variables:
  alarm
Consider adding
  importFrom("utils", "alarm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘lattice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
svd3dplot: no visible global function definition for ‘wireframe’
svd3dplot: no visible global function definition for ‘levelplot’
Undefined global functions or variables:
  levelplot wireframe
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
startHttpServer : <anonymous> : Rjsonp: no visible global function
  definition for ‘localeToCharset’
Undefined global functions or variables:
  localeToCharset
Consider adding
  importFrom("utils", "localeToCharset")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
.onAttach : svBrowser: no visible global function definition for
  ‘browseURL’
.onAttach: no visible global function definition for ‘loadhistory’
Undefined global functions or variables:
  browseURL loadhistory
Consider adding
  importFrom("utils", "browseURL", "loadhistory")
to your NAMESPACE file.
File ‘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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
svycox.calibrate: no visible global function definition for ‘quantile’
svycox.calibrate: no visible binding for global variable ‘median’
svycox.calibrate: no visible global function definition for
  ‘as.formula’
svycox.calibrate: no visible global function definition for ‘arrows’
svycox.calibrate: no visible global function definition for ‘abline’
svycox.nomogram: no visible global function definition for ‘predict’
svycox.nomogram: no visible global function definition for ‘as.formula’
svycox.validate : internal.validate.func: no visible global function
  definition for ‘as.formula’
svycox.validate : internal.validate.func: no visible global function
  definition for ‘formula’
Undefined global functions or variables:
  abline arrows as.formula formula median predict quantile
Consider adding
  importFrom("graphics", "abline", "arrows")
  importFrom("stats", "as.formula", "formula", "median", "predict",
             "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tidyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘swephRdata’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘mapdata’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages in Depends field not imported from:
  ‘MASS’ ‘fda’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fj_pl: no visible global function definition for ‘getbasismatrix’
fj_pl: no visible global function definition for ‘create.bspline.basis’
fj_pl: no visible global function definition for ‘getbasispenalty’
forward_backward.quantities : <anonymous>: no visible global function
  definition for ‘dnorm’
function_cases1AND2: no visible global function definition for ‘dnorm’
function_cases3AND4: no visible global function definition for ‘dnorm’
pij_iid: no visible global function definition for ‘dnorm’
pilj: no visible global function definition for ‘dnorm’
updateLambda: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  create.bspline.basis dnorm getbasismatrix getbasispenalty optimize
Consider adding
  importFrom("stats", "dnorm", "optimize")
to your NAMESPACE file.
Running examples in ‘switchr-Ex.R’ failed
The error most likely occurred in:

> ### Name: libManifest
> ### Title: libManifest
> ### Aliases: libManifest libManifest,missing-method libManifest,missing
> ###   libManifest,character-method libManifest,character
> ###   libManifest,SwitchrCtx-method libManifest,SwitchrCtx
> 
> ### ** Examples
> 
> man = libManifest()
Bioconductor version '3.14' requires R version '4.1'; use
  `BiocManager::install(version = '3.15')` with R version 4.2; see
  https://bioconductor.org/install
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://cloud.r-project.org


Execution halted
'LazyData' is specified without a 'data' directory
Undeclared package ‘sp’ in Rd xrefs
Package suggested but not available for checking: ‘cplexAPI’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
Note: found 1 marked UTF-8 string
Package suggested but not available for checking: ‘cplexAPI’
Packages suggested but not available for checking: 'cplexAPI', 'clpAPI'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
'LazyData' is specified without a 'data' directory
symbol: no visible global function definition for ‘plot.new’
symbol: no visible global function definition for ‘plot.window’
symbol: no visible global function definition for ‘axis’
symbol: no visible global function definition for ‘box’
symbol: no visible global function definition for ‘title’
symbol: no visible global function definition for ‘rainbow’
symbol: no visible global function definition for ‘hsv’
symbol: no visible global function definition for ‘rect’
symbol: no visible global function definition for ‘polygon’
symbol: no visible global function definition for ‘lines’
symbol: no visible global function definition for ‘text’
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window polygon rainbow rect text
  title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "polygon", "rect", "text", "title")
to your NAMESPACE file.
Rd file 'symbol.Rd':
  \usage lines wider than 90 characters:
     symbol(df, type="star", colin=NULL, colout=NULL, colin2=NA, colout2=1, ssize=NULL, labels=0, labelsize=0.6,
            scheme=1, sortby=0, descending=FALSE, coorx=NULL, coory=NULL, lty=1, main=NULL, sub=NULL, xlab=NULL, ylab=NULL,
            add=FALSE, xlim=NULL, ylim=NULL, facew=0.5, faceh=0.5, eyes=0.5, eyed=0.5, mouthw=0.5, mouthc=0.5, brows=0.5,
            browp=0.5, nosel=0.5, nosew=0.5, ears=0.5, pupils=0.5, body=0.5, limb1=0.5, limb2=0.5, limb3=0.5, limb4=0.5, defcol=NA)

These lines will be truncated in the PDF manual.
installed size is 32.6Mb
  sub-directories of 1Mb or more:
    libs  31.8Mb
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
possible bashism in configure line 12 (echo -n):
  echo -n "  checking for Sun Studio compiler..."
  possible bashism in configure line 22 (echo -n):
  echo -n "  checking for OS..."
Package in Depends field not imported from: ‘fields’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cwt_fw: no visible global function definition for ‘fft’
cwt_iw: no visible global function definition for ‘fft’
est_riskshrink_thresh: no visible global function definition for
  ‘median’
Undefined global functions or variables:
  fft median
Consider adding
  importFrom("stats", "fft", "median")
to your NAMESPACE file.
File ‘SynchWave/libs/SynchWave.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard file/directory found at top level:
  ‘doc’
'library' or 'require' calls to packages already attached by Depends:
  ‘tcltk’ ‘tkrplot’
  Please remove these calls from your code.
Rd file 'acshgral.rd':
  \examples lines wider than 100 characters:
       #Display relationships into a parenthetical notation. You can track the indices of the species in the

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

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

These lines will be truncated in the PDF manual.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    extdata   3.4Mb
Namespace in Imports field not imported from: ‘metR’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
mainNetFunction: no visible global function definition for ‘png’
mainNetFunction: no visible global function definition for ‘lines’
mainNetFunction: no visible global function definition for ‘legend’
mainNetFunction: no visible global function definition for ‘dev.off’
plotROC: no visible global function definition for ‘lines’
simulatedData: no visible global function definition for ‘rpois’
simulatedData : <anonymous>: no visible global function definition for
  ‘rpois’
simulatedData : rlognormpois: no visible global function definition for
  ‘rnorm’
simulatedData : rlognormpois: no visible global function definition for
  ‘rpois’
Undefined global functions or variables:
  dev.off legend lines png rnorm rpois
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'library' or 'require' calls in package code:
  ‘LowRankQP’ ‘rgenoud’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
fn.V: no visible global function definition for ‘LowRankQP’
gaps.plot: no visible global function definition for ‘abline’
path.plot: no visible global function definition for ‘lines’
path.plot: no visible global function definition for ‘abline’
path.plot: no visible global function definition for ‘legend’
synth: no visible binding for global variable ‘sd’
synth: no visible binding for global variable ‘var’
synth: no visible global function definition for ‘LowRankQP’
Undefined global functions or variables:
  LowRankQP abline legend lines sd var
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "sd", "var")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘Ecdat’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
'LazyData' is specified without a 'data' directory
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
Undeclared package ‘HSAUR3’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
.checkDimAndTest: no visible global function definition for
  ‘chisq.test’
.checkDimAndTest: no visible global function definition for
  ‘fisher.test’
plotTable1Heatmap: no visible global function definition for ‘par’
plotTable1Heatmap: no visible global function definition for ‘image’
plotTable1Heatmap: no visible global function definition for ‘abline’
plotTable1Heatmap: no visible global function definition for ‘axis’
plotTable1Heatmap: no visible global function definition for ‘text’
plotTable1Heatmap: no visible global function definition for ‘legend’
plotTable1Heatmap: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box chisq.test fisher.test image legend par text
Consider adding
  importFrom("graphics", "abline", "axis", "box", "image", "legend",
             "par", "text")
  importFrom("stats", "chisq.test", "fisher.test")
to your NAMESPACE file.
Found the following files/directories:
  ‘.xls’ ‘attenu.xls’ ‘chick1.xls’ ‘chick2.xls’ ‘generic1.xls’
  ‘hands.xls’ ‘table1.xls’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 81 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘stringr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘icesAdvice’ in Rd xrefs
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.
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘devEMF’ ‘segmented’ ‘smoother’ ‘tools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   4.5Mb
Undeclared package ‘mirt’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jiebaR’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘spruce.taper.pars.rdata’
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Running examples in ‘targeted-Ex.R’ failed
The error most likely occurred in:

> ### Name: scoring
> ### Title: Predictive model scoring
> ### Aliases: scoring
> 
> ### ** Examples
> 
> data(iris)
> set.seed(1)
> dat <- csplit(iris,2)
Error in `[.data.frame`(x, ii) : undefined columns selected
Calls: csplit -> lapply -> FUN -> [ -> [.data.frame
Execution halted
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'library' or 'require' calls in package code:
  ‘gdata’ ‘ggplot2’ ‘grid’ ‘lattice’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘dplyr’ ‘igraph’ ‘tm’ ‘wordcloud2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tashudata’
Namespaces in Imports field not imported from:
  ‘drat’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘GEOmap’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘duckdb’ ‘memoise’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘jsonlite’ ‘knitr’ ‘lazyeval’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘taxa’
  All declared Imports should be used.
Note: found 137 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 596 marked UTF-8 strings
File ‘tbart/libs/tbart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
BootTree: no visible global function definition for ‘hclust’
BootTree: no visible global function definition for ‘dist’
BootTree: no visible global function definition for ‘as.dist’
BootTree: no visible global function definition for ‘cor’
BootTree: no visible binding for global variable ‘var’
Pgpd: no visible global function definition for ‘optim’
Pgpd : <anonymous>: no visible global function definition for ‘optim’
Pgpd: no visible global function definition for ‘var’
Pgpd: no visible global function definition for ‘rnorm’
Pgpd: no visible global function definition for ‘quantile’
Pvalue: no visible global function definition for ‘rnorm’
SigTree: no visible global function definition for ‘data’
TreeStat: no visible global function definition for ‘hclust’
TreeStat: no visible global function definition for ‘as.dist’
TreeStat: no visible global function definition for ‘dist’
TreeStat: no visible global function definition for ‘cor’
plot.best: no visible global function definition for ‘hclust’
plot.best: no visible global function definition for ‘as.dist’
plot.best: no visible global function definition for ‘dist’
plot.best: no visible global function definition for ‘cor’
treetext: no visible global function definition for ‘par’
treetext: no visible global function definition for ‘text’
Undefined global functions or variables:
  as.dist cor data dist hclust optim par quantile rnorm text var
Consider adding
  importFrom("graphics", "par", "text")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "optim",
             "quantile", "rnorm", "var")
  importFrom("utils", "data")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘quadprog’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tcgsaseq’
Unknown package ‘tcgsaseq’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘open-closed-loop-control.Rmd’ using rmarkdown
OMP: Warning #96: Cannot form a team with 8 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).
Quitting from lines 151-157 (open-closed-loop-control.Rmd) 
Error: processing vignette 'open-closed-loop-control.Rmd' failed with diagnostics:
dataframe updates must have column named 'time'
--- failed re-building ‘open-closed-loop-control.Rmd’

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

--- re-building ‘user-defined-ode-pkmod.Rmd’ using rmarkdown
--- finished re-building ‘user-defined-ode-pkmod.Rmd’

SUMMARY: processing the following file failed:
  ‘open-closed-loop-control.Rmd’

Error: Vignette re-building failed.
Execution halted
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc  11.2Mb
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘psych’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    tklibs   4.9Mb
Malformed Description field: should contain one or more complete sentences.
Undeclared package ‘Rtsne’ in Rd xrefs
cluster_cutoff_at_first_empty_bin: no visible global function
  definition for ‘hist’
mapper1D: no visible global function definition for ‘dist’
mapper1D: no visible global function definition for ‘as.dist’
mapper1D: no visible global function definition for ‘hclust’
mapper1D: no visible global function definition for ‘cutree’
mapper2D: no visible global function definition for ‘dist’
mapper2D: no visible global function definition for ‘as.dist’
mapper2D: no visible global function definition for ‘hclust’
mapper2D: no visible global function definition for ‘cutree’
Undefined global functions or variables:
  as.dist cutree dist hclust hist
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cutree", "dist", "hclust")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  28.1Mb
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘TDboost/libs/TDboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘RSEIS’ ‘pracma’ ‘signal’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CalcCorners: no visible global function definition for ‘abline’
ConvDiffCoef: no visible global function definition for ‘pascal’
ConvolveTrace: no visible global function definition for ‘filter’
DeconTrace: no visible global function definition for ‘as.Zpg’
DeconTrace: no visible global function definition for ‘butter’
DeconTrace: no visible global function definition for ‘filter’
GetDPZ: no visible global function definition for ‘data’
MakeDPZ: no visible global function definition for ‘bilinear’
MakeDPZ: no visible global function definition for ‘fft’
MakeDPZ: no visible global function definition for ‘lines’
MakeDPZ: no visible global function definition for ‘legend’
MatchCoefDPZ : CalcMisfit: no visible global function definition for
  ‘fft’
MatchCoefDPZ : CalcMisfit: no visible global function definition for
  ‘filter’
MatchCoefDPZ : generate: no visible global function definition for
  ‘runif’
MatchCoefDPZ : generate: no visible global function definition for
  ‘rnorm’
MatchCoefDPZ: no visible global function definition for ‘fft’
MatchCoefDPZ: no visible global function definition for ‘filter’
MatchCoefDPZ: no visible global function definition for ‘Zpg’
MatchCoefDPZ: no visible global function definition for ‘lines’
MatchCoefDPZ: no visible global function definition for ‘abline’
Metropolis: no visible global function definition for ‘runif’
PZ2Coef: no visible global function definition for ‘Poly’
PlotResp: no visible global function definition for ‘fft’
PlotResp: no visible global function definition for ‘filter’
PlotResp: no visible global function definition for ‘lines’
Undefined global functions or variables:
  Poly Zpg abline as.Zpg bilinear butter data fft filter legend lines
  pascal rnorm runif
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "fft", "filter", "rnorm", "runif")
  importFrom("utils", "data")
to your NAMESPACE file.
Undeclared package ‘survivalROC’ in Rd xrefs
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    apps   3.2Mb
    libs   9.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘R2wd’
Undeclared package ‘scales’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘teigen-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot.teigen
> ### Title: plot.teigen: Plotting Function for tEIGEN Objects
> ### Aliases: plot.teigen
> 
> ### ** Examples
> 
> set.seed(2521)
> tfaith <- teigen(faithful, models = "CCCC", Gs = 1:4, verbose = FALSE)
Error in colMeans(x, na.rm = TRUE) : 'x' must be numeric
Calls: teigen -> scale -> scale.default -> colMeans
Execution halted
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  14.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    libs      1.4Mb
    telemac   1.0Mb
Undeclared package ‘tibble’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘tempR-Ex.R’ failed
The error most likely occurred in:

> ### Name: tds.diff.plot
> ### Title: Plot TDS difference curves
> ### Aliases: tds.diff.plot
> 
> ### ** Examples
> 
> # example using 'bars' data set
> bars.m <- aggregate(bars[, -c(1:4)], list(samples = bars$sample, attribute = bars$attribute), mean)
> bars.m <- bars.m[order(bars.m$sample, bars.m$attribute), ]
> attributes <- unique(bars$attribute)
> times <- get.times(colnames(bars.m)[-c(1:2)])
> bar1 <- bars.m[bars.m$sample == 1, -c(1:2)]
> bar2 <- bars.m[bars.m$sample == 2, -c(1:2)]
> diff.1vs2 <- get.smooth(bar1 - bar2, low.bound = -1, up.bound = 1)
Error in xy.coords(x, y, setLab = FALSE) : 
  'list' object cannot be coerced to type 'double'
Calls: get.smooth -> <Anonymous> -> xy.coords
Execution halted
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Undeclared package ‘tfestimators’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
TER.deesc.1.B : A1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B : A1.f: no visible binding for global variable ‘ID’
TER.deesc.1.B : A2.n.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B : A2.n.f: no visible binding for global variable ‘ID’
TER.deesc.1.B: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B: no visible binding for global variable ‘ID’
TER.deesc.A.B : A1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A1.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : A3.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A3.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : A2.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A2.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : B1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : B1.f: no visible binding for global variable ‘ID’
TER.deesc.A.B: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B: no visible binding for global variable ‘ID’
Undefined global functions or variables:
  ID
'LazyData' is specified without a 'data' directory
installed size is 37.2Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  34.7Mb
File ‘TESS/libs/TESS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘ExtinctionRateChanges.txt’ ‘ExtinctionRates.txt’
  ‘MassExtinctionTimes.txt’ ‘SpeciationRateChanges.txt’
  ‘SpeciationRates.txt’ ‘SurvivalProbabilities.txt’ ‘analysis_conifer’
  ‘input_tree.tre’ ‘run_1’ ‘run_2’ ‘samples_numCategories.txt’
Requires orphaned package: ‘mfp’
Found the following files/directories:
  ‘par-7269706c6579’
Running ‘testthat.R’ [11s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(testdat)
  
  Attaching package: 'testdat'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  > 
  > test_check("testdat")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-reporter_excel.R:44:3): excel_results ─────────────────────────
  `x_xl_summary` not equal to `xl_summary`.
  Names: 6 string mismatches
  Component 2: 'is.NA' value mismatch: 0 in current 1 in target
  Component 3: 'is.NA' value mismatch: 0 in current 1 in target
  Component 4: 'is.NA' value mismatch: 0 in current 1 in target
  Component 5: 'is.NA' value mismatch: 0 in current 1 in target
  Component 6: 'is.NA' value mismatch: 0 in current 1 in target
  ── Failure (test-reporter_excel.R:45:3): excel_results ─────────────────────────
  `x_xl_failing` not equal to `xl_failing`.
  Names: 8 string mismatches
  Attributes: < Component "row.names": Numeric: lengths (1, 2) differ >
  Component 1: Lengths (1, 2) differ (string compare on first 1)
  Component 2: Lengths (1, 2) differ (string compare on first 1)
  Component 3: Lengths (1, 2) differ (string compare on first 1)
  Component 4: Lengths (1, 2) differ (string compare on first 1)
  Component 4: 1 string mismatch
  Component 5: Lengths (1, 2) differ (string compare on first 1)
  Component 5: 1 string mismatch
  ...
  ── Failure (test-reporter_excel.R:46:3): excel_results ─────────────────────────
  names(x_xl_passing) not equal to names(xl_failing).
  target is NULL, current is character
  ── Failure (test-reporter_excel.R:47:3): excel_results ─────────────────────────
  nrow(x_xl_passing) not equal to 0.
  target is NULL, current is numeric
  
  [ FAIL 4 | WARN 1 | SKIP 0 | PASS 164 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘gurobi’
Running examples in ‘TestDesign-Ex.R’ failed
The error most likely occurred in:

> ### Name: eap
> ### Title: Compute expected a posteriori estimates of theta
> ### Aliases: eap eap,item_pool-method EAP EAP,test-method
> ###   EAP,test_cluster-method
> 
> ### ** Examples
> 
> eap(itempool_fatigue, resp = resp_fatigue_data[10, ])
Error in resp[i] + 1 : non-numeric argument to binary operator
Calls: eap -> eap
Execution halted
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘mnlogit’
Undeclared packages ‘h2o’, ‘eha’, ‘mfx’, ‘betareg’, ‘brglm’, ‘censReg’, ‘ergm’, ‘latentnet’, ‘fGarch’, ‘gee’, ‘geepack’, ‘gmm’, ‘robustbase’, ‘gnm’, ‘pscl’, ‘robust’, ‘sna’, ‘lqmm’, ‘rms’, ‘erer’, ‘mhurdle’, ‘oglmx’, ‘panelAR’, ‘pglm’, ‘relevent’, ‘quantreg’, ‘spatialreg’, ‘sampleSelection’, ‘RSiena’, ‘simex’, ‘tergm’, ‘survey’, ‘systemfit’, ‘metaSEM’ in Rd xrefs
Unknown packages ‘mnlogit’, ‘panelAR’ in Rd xrefs
Note: found 3 marked UTF-8 strings
Note: found 75 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    2.9Mb
    libs   4.0Mb
Undeclared package ‘NLP’ in Rd xrefs
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.
Undeclared package ‘gsubfn’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘parallel’ ‘tidyr’
  All declared Imports should be used.
Note: found 40 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
Undeclared package ‘tm’ in Rd xrefs
phyper_right: no visible global function definition for ‘dhyper’
progression: no visible global function definition for ‘density’
progression: no visible global function definition for ‘points’
progression: no visible global function definition for ‘legend’
progression: no visible global function definition for ‘text’
specificities.distribution.plot: no visible global function definition
  for ‘dhyper’
specificities.distribution.plot: no visible global function definition
  for ‘Axis’
specificities.distribution.plot: no visible global function definition
  for ‘arrows’
specificities.distribution.plot: no visible global function definition
  for ‘text’
specificities.distribution.plot: no visible global function definition
  for ‘title’
specificities.probabilities.vector: no visible global function
  definition for ‘phyper’
Undefined global functions or variables:
  Axis arrows density dhyper legend phyper points text title
Consider adding
  importFrom("graphics", "Axis", "arrows", "legend", "points", "text",
             "title")
  importFrom("stats", "density", "dhyper", "phyper")
to your NAMESPACE file.
Note: found 3 marked UTF-8 strings
Running ‘testthat.R’ [8s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library(testthat)
  > library(text)
  This is text (version 0.9.10). 
  Text is new and still rapidly improving. 
  Newer versions may have improved functions and updated defaults to reflect current understandings of the state-of-the-art. 
  Please send us feedback based on your experience.
  > 
  > test_check("text")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (29)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_2_textTrain.R:560:3): textTrainRandomForest adding wordembeddings together ──
  <subscriptOutOfBoundsError/error/condition>
  Error in `y.mat[, 2]`: subscript out of bounds
  Backtrace:
       █
    1. └─text::textTrainRandomForest(...) test_2_textTrain.R:560:2
    2.   └─furrr::future_map(...)
    3.     └─furrr:::furrr_map_template(...)
    4.       └─furrr:::furrr_template(...)
    5.         ├─future::value(futures)
    6.         └─future:::value.list(futures)
    7.           ├─future::resolve(...)
    8.           └─future:::resolve.list(...)
    9.             └─future:::signalConditionsASAP(obj, resignal = FALSE, pos = ii)
   10.               └─future:::signalConditions(...)
  
  [ FAIL 1 | WARN 0 | SKIP 29 | PASS 0 ]
  Error: Test failures
  Execution halted
Undeclared package ‘tm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared packages ‘tm’, ‘textreadr’ in Rd xrefs
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
ParseTrueFX: no visible global function definition for ‘read.csv’
TrueFXRef: no visible global function definition for ‘download.file’
TrueFXRef: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL download.file read.csv
Consider adding
  importFrom("utils", "browseURL", "download.file", "read.csv")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘akima’ in Rd xrefs
Namespace in Imports field not imported from: ‘ggm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    rda    7.1Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘glmnet’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Thinknum: no visible global function definition for ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘crayon’ ‘purrr’ ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
coef_traceplot: no visible global function definition for ‘rainbow’
coef_traceplot: no visible global function definition for ‘abline’
coef_traceplot : <anonymous>: no visible global function definition for
  ‘lines’
coef_traceplot: no visible global function definition for ‘text’
ee.GEE.aux : <anonymous>: no visible global function definition for
  ‘combn’
Undefined global functions or variables:
  abline combn lines rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc           1.7Mb
    htmlwidgets   2.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
summary.tsls: no visible global function definition for ‘printCoefmat’
threesls: no visible global function definition for ‘cor’
threesls: no visible global function definition for ‘pt’
tsls.formula: no visible global function definition for ‘model.matrix’
tsls.formula: no visible global function definition for
  ‘model.response’
Undefined global functions or variables:
  cor model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.matrix", "model.response",
             "printCoefmat", "pt")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
installed size is 40.5Mb
  sub-directories of 1Mb or more:
    libs  40.0Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘knitr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
.LoadTickDataHK: no visible global function definition for ‘read.csv’
.LoadTickDataSHSZ: no visible global function definition for ‘read.csv’
DrawDown: no visible global function definition for ‘na.omit’
PerformanceReport: no visible global function definition for
  ‘aggregate’
PerformanceReport: no visible global function definition for ‘sd’
Undefined global functions or variables:
  aggregate na.omit read.csv sd
Consider adding
  importFrom("stats", "aggregate", "na.omit", "sd")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
newTiddler: no visible global function definition for ‘new’
twImage: no visible global function definition for ‘new’
twLink: no visible global function definition for ‘new’
twList: no visible global function definition for ‘new’
twTable: no visible global function definition for ‘new’
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘badger’ ‘ggplot2’ ‘lubridate’ ‘scales’ ‘xgboost’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rsvg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘autostats’ ‘badger’ ‘framecleaner’ ‘presenter’ ‘tidybins’ ‘validata’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘graphics’ ‘utils’
  All declared Imports should be used.
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared packages ‘fastDummies’, ‘sjmisc’ in Rd xrefs
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidyfst)
  
  Life's short, use R.
  
  > 
  > test_check("tidyfst")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-nest_dt.R:34:3): unnest ───────────────────────────────────────
  mtcars %>% nest_dt("cyl") %>% unnest_dt(ndt) not equal to ...[].
  Different number of rows
  Different number of columns
  Different column names
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 180 ]
  Error: Test failures
  Execution halted
Undeclared packages ‘tidyfst’, ‘tidyr’, ‘fastDummies’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 122 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘decorators’ ‘microservices’ ‘usethat’
  All declared Imports should be used.
Undeclared package ‘slam’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mix’
  All declared Imports should be used.
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘Evomorph’ ‘cowplot’ ‘factoextra’ ‘gridExtra’ ‘lme4’ ‘lsr’ ‘plotly’
  ‘png’ ‘shapes’
  All declared Imports should be used.
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘hardhat’ ‘modeldata’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Namespace in Imports field not imported from: ‘janitor’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 24 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared package ‘mclust’ in Rd xrefs
Found the following significant warnings:
  ../inst/include/tidysq/Sequence.h:20:53: warning: 'iterator<std::bidirectional_iterator_tag, unsigned char>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/tidysq.Rcheck/00install.out’ for details.
installed size is 51.3Mb
  sub-directories of 1Mb or more:
    libs  50.4Mb
Note: found 113 marked UTF-8 strings
Note: found 34206 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   4.4Mb
Note: found 61 marked UTF-8 strings
Running ‘testthat.R’ [37s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidytransit)
  > 
  > test_check("tidytransit")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (8)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-spatial.R:96:3): sf_as_tbl ──────────────────────────────────────
  Error in `cbind(as.numeric(obj[, xy_cols[1], drop = TRUE]), as.numeric(obj[, 
      xy_cols[2], drop = TRUE]))`: 'list' object cannot be coerced to type 'double'
  Backtrace:
      █
   1. └─tidytransit::sf_as_tbl(duke_sf) test-spatial.R:96:2
   2.   ├─dplyr::as_tibble(sf_lines_to_df(gtfs_obj$shapes))
   3.   └─tidytransit:::sf_lines_to_df(gtfs_obj$shapes)
   4.     └─base::lapply(...)
   5.       └─tidytransit:::FUN(X[[i]], ...)
   6.         └─geodist::geodist(df[c("shape_pt_lon", "shape_pt_lat")], sequential = T)
   7.           └─geodist:::convert_to_matrix(x)
   8.             └─base::cbind(...)
  
  [ FAIL 1 | WARN 0 | SKIP 8 | PASS 169 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘dtplyr’ ‘googledrive’ ‘googlesheets4’
  All declared Imports should be used.
Running examples in ‘tidyvpc-Ex.R’ failed
The error most likely occurred in:

> ### Name: binning
> ### Title: Binning methods for Visual Predictive Check (VPC)
> ### Aliases: binning binning.tidyvpcobj
> 
> ### ** Examples
> 
> require(magrittr)
Loading required package: magrittr
> 
>  # Binning on x-variable NTIME
> vpc <- observed(obs_data, x=TIME, y=DV) %>%
+     simulated(sim_data, y=DV) %>%
+     binning(bin = NTIME) %>%
+     vpcstats()
>     
>  # Binning using ntile and xmean for midpoint
> vpc <- observed(obs_data, x=TIME, y=DV) %>%
+     simulated(sim_data, y=DV) %>%
+     binning(bin = "ntile", nbins = 8, xbin = "xmean") %>%
+     vpcstats()
>     
>  # Binning using centers
> vpc <- observed(obs_data, x=TIME, y=DV) %>%
+     simulated(sim_data, y=DV) %>%
+     binning(bin = "centers", centers = c(1,3,5,7)) %>%
+     vpcstats()
>         
>  # Different Binning for each level of Strata
> vpc <- observed(obs_data, x=TIME, y=DV) %>%
+     simulated(sim_data, y=DV) %>%
+     stratify(~ GENDER) %>%
+     binning(stratum = list(GENDER = "M"), bin = "jenks", nbins = 5, by.strata = TRUE) %>%
+     binning(stratum = list(GENDER = "F"), bin = "pam", nbins = 4, by.strata = TRUE) %>%
+     vpcstats()
>     
>  # Binning Categorical DV using rounded time variable
>   
>   vpc <- observed(obs_cat_data, x = agemonths, y = zlencat ) %>%
+       simulated(sim_cat_data, y = DV) %>%
+       binning(bin = round(agemonths, 0)) %>%
+       vpcstats(vpc.type = "categorical")
Error in fastDummies::dummy_columns(obs, select_columns = "y") : 
  select_columns is/are not in data. Please check data and spelling.
Calls: %>% ... vpcstats.tidyvpcobj -> [ -> [.data.table -> eval -> eval -> <Anonymous>
Execution halted
Running ‘testthat.R’ [16s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidyvpc)
  > 
  > test_check("tidyvpc")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (4)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-binning.R:34:3): cat obs vpcstats is correct ────────────────────
  Error in `fastDummies::dummy_columns(obs, select_columns = "y")`: select_columns is/are not in data. Please check data and spelling.
  Backtrace:
      █
   1. ├─tidyvpc::vpcstats(vpc, vpc.type = "categorical") test-binning.R:34:2
   2. └─tidyvpc:::vpcstats.tidyvpcobj(vpc, vpc.type = "categorical")
   3.   ├─obs[, fastDummies::dummy_columns(obs, select_columns = "y")]
   4.   └─data.table:::`[.data.table`(...)
   5.     └─base::eval(jsub, SDenv, parent.frame())
   6.       └─base::eval(jsub, SDenv, parent.frame())
   7.         └─fastDummies::dummy_columns(obs, select_columns = "y")
  ── Error (test-binning.R:59:3): cat obs strat vpcstats is correct ──────────────
  Error in `fastDummies::dummy_columns(obs, select_columns = "y")`: select_columns is/are not in data. Please check data and spelling.
  Backtrace:
      █
   1. ├─tidyvpc::vpcstats(vpc, vpc.type = "categorical") test-binning.R:59:2
   2. └─tidyvpc:::vpcstats.tidyvpcobj(vpc, vpc.type = "categorical")
   3.   ├─obs[, fastDummies::dummy_columns(obs, select_columns = "y")]
   4.   └─data.table:::`[.data.table`(...)
   5.     └─base::eval(jsub, SDenv, parent.frame())
   6.       └─base::eval(jsub, SDenv, parent.frame())
   7.         └─fastDummies::dummy_columns(obs, select_columns = "y")
  
  [ FAIL 2 | WARN 0 | SKIP 4 | PASS 5 ]
  Error: Test failures
  Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Malformed Description field: should contain one or more complete sentences.
Error(s) in re-building vignettes:
--- re-building ‘tikzDevice.Rnw’ using knitr
Error: processing vignette 'tikzDevice.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'tikzDevice.tex' failed.
LaTeX errors:
! Package xcolor Error: Undefined color `warningcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `warningcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
--- failed re-building ‘tikzDevice.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  ../inst/tiledb/include/tiledb/config.h:52:32: warning: 'iterator<std::forward_iterator_tag, const std::pair<std::string, std::string>>' is deprecated [-Wdeprecated-declarations]
  ../inst/tiledb/include/tiledb/object_iter.h:152:21: warning: 'iterator<std::forward_iterator_tag, const tiledb::Object>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/tiledb.Rcheck/00install.out’ for details.
installed size is 53.9Mb
  sub-directories of 1Mb or more:
    libs     9.9Mb
    tiledb  42.0Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Note: found 341 marked UTF-8 strings
Codoc mismatches from documentation object 'identical':
identical
  Code: function(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.set =
                 TRUE, ignore.bytecode = TRUE, ignore.environment =
                 FALSE, ignore.srcref = TRUE, extptr.as.ref = FALSE)
  Docs: function(x, y, num.eq = TRUE, single.NA = TRUE, attrib.as.set =
                 TRUE, ignore.bytecode = TRUE, ignore.environment =
                 FALSE, ignore.srcref = TRUE)
  Argument names in code not in docs:
    extptr.as.ref
Namespace in Imports field not imported from: ‘lwgeom’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘shiny’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘ggplot2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
timeline: no visible global function definition for ‘ggplot’
timeline: no visible global function definition for ‘geom_segment’
timeline: no visible global function definition for ‘aes_string’
timeline: no visible global function definition for ‘geom_rect’
timeline: no visible global function definition for ‘geom_text’
timeline: no visible global function definition for ‘theme’
timeline: no visible global function definition for ‘element_blank’
timeline: no visible global function definition for ‘xlab’
timeline: no visible global function definition for ‘ylab’
timeline: no visible global function definition for ‘xlim’
timeline: no visible global function definition for
  ‘scale_y_continuous’
timeline: no visible global function definition for ‘geom_point’
timeline: no visible global function definition for ‘scale_color_grey’
timeline: no visible global function definition for ‘geom_hline’
Undefined global functions or variables:
  aes_string element_blank geom_hline geom_point geom_rect geom_segment
  geom_text ggplot scale_color_grey scale_y_continuous theme xlab xlim
  ylab
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'library' or 'require' calls in package code:
  ‘ggplot2’ ‘plyr’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Matrix’ ‘lubridate’ ‘timeDate’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
is.Bizday: no visible global function definition for ‘isWeekday’
plotCalendarHeatmap: no visible global function definition for ‘ddply’
plotCalendarHeatmap: no visible global function definition for ‘.’
plotCalendarHeatmap: no visible binding for global variable ‘year’
plotCalendarHeatmap: no visible binding for global variable ‘month’
plotCalendarHeatmap: no visible binding for global variable ‘week’
plotCalendarHeatmap: no visible global function definition for ‘ggplot’
plotCalendarHeatmap: no visible global function definition for ‘aes’
plotCalendarHeatmap: no visible binding for global variable ‘monthweek’
plotCalendarHeatmap: no visible binding for global variable ‘weekday’
plotCalendarHeatmap: no visible global function definition for
  ‘geom_tile’
plotCalendarHeatmap: no visible global function definition for
  ‘facet_grid’
plotCalendarHeatmap: no visible global function definition for
  ‘scale_fill_gradientn’
projectDate: no visible global function definition for ‘holidayNYSE’
projectDate: no visible global function definition for
  ‘sparse.model.matrix’
Undefined global functions or variables:
  . aes ddply facet_grid geom_tile ggplot holidayNYSE isWeekday month
  monthweek scale_fill_gradientn sparse.model.matrix week weekday year
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'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.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Note: found 2750 marked UTF-8 strings
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.
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
drawGraph: no visible global function definition for ‘pdf’
drawGraph: no visible global function definition for ‘par’
drawGraph: no visible global function definition for ‘segments’
drawGraph: no visible global function definition for ‘lines’
drawGraph: no visible global function definition for ‘text’
drawGraph: no visible global function definition for ‘dev.off’
drugRank: no visible global function definition for ‘aggregate’
floating2: no visible global function definition for ‘cor’
timma: no visible global function definition for ‘median’
timma: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  aggregate cor dev.off lines median par pdf segments text write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "segments", "text")
  importFrom("stats", "aggregate", "cor", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
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.
Found the following files/directories:
  ‘_paramEst.txt’
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Namespaces in Imports field not imported from:
  ‘cpp11’ ‘dplyr’ ‘magrittr’ ‘stringi’
  All declared Imports should be used.
Note: found 384749 marked UTF-8 strings
Non-standard files/directories found at top level:
  ‘DESCRIPTION.orig’ ‘README.rst’
tipom.car: no visible global function definition for ‘abline’
tipom.car: no visible global function definition for ‘axis’
tipom.heat: no visible global function definition for ‘image’
tipom.heat: no visible global function definition for ‘gray’
tipom.lw: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis gray image
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "image")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘snow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘base64enc’
  All declared Imports should be used.
Undeclared package ‘tibble’ in Rd xrefs
'LazyData' is specified without a 'data' directory
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.
Undeclared package ‘modeltools’ in Rd xrefs
'library' or 'require' call to ‘mvtnorm’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
EMN: no visible global function definition for ‘dmvnorm’
EMN: no visible global function definition for ‘pmvnorm’
EMT: no visible global function definition for ‘GenzBretz’
EMT: no visible global function definition for ‘dmvt’
EMT: no visible global function definition for ‘pmvt’
MomemNT: no visible global function definition for ‘pnorm’
MomemNT: no visible global function definition for ‘dnorm’
MomemNT: no visible global function definition for ‘pmvnorm’
MomemNT: no visible global function definition for ‘dmvnorm’
TT.moment: no visible global function definition for ‘GenzBretz’
TT.moment: no visible global function definition for ‘pmvt’
TT.moment: no visible global function definition for ‘dt’
TT.moment: no visible global function definition for ‘pt’
TT.moment: no visible global function definition for ‘dmvt’
cdfNI: no visible global function definition for ‘pnorm’
cdfNI: no visible global function definition for ‘pt’
inits: no visible global function definition for ‘lm’
Undefined global functions or variables:
  GenzBretz dmvnorm dmvt dnorm dt lm pmvnorm pmvt pnorm pt
Consider adding
  importFrom("stats", "dnorm", "dt", "lm", "pnorm", "pt")
to your NAMESPACE file.
Rd file 'UTIdata.Rd':
  \examples lines wider than 100 characters:
     x = cbind((UTIdata$Fup==0)+0, (UTIdata$Fup==1)+0, (UTIdata$Fup==3)+0, (UTIdata$Fup==6)+0, (UTIdata$Fup==9)+0, (UTIdata$Fup==12)+0, (UTI ... [TRUNCATED]

These lines will be truncated in the PDF manual.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Found the following significant warnings:
  Warning: replacing previous import ‘bit64::hashtab’ by ‘utils::hashtab’ when loading ‘tlsh’
See ‘/data/gannet/ripley/R/packages/tests-clang/tlsh.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘sp’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    examples  12.5Mb
    include    3.0Mb
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    libs  21.0Mb
Note: found 134043 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
Undeclared packages ‘tm.plugin.dc’, ‘readtext’, ‘graph’, ‘tau’, ‘tokenizers’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘PROJ’
  All declared Imports should be used.
Note: found 160 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘stm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘corpus.JSS.papers’
Package suggested but not available for checking: ‘gWidgets2RGtk2’

Suggests orphaned package: ‘RGtk2’
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rappdirs’ ‘withr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘stringr’ ‘torch’ ‘torchvision’ ‘zip’
  All declared Imports should be used.
installed size is 110.7Mb
  sub-directories of 1Mb or more:
    R       4.7Mb
    help    1.6Mb
    libs  103.8Mb
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘toscaData’
Malformed Description field: should contain one or more complete sentences.
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.
Namespaces in Imports field not imported from:
  ‘R6’ ‘jmvcore’
  All declared Imports should be used.
Note: found 100 marked Latin-1 strings
  Note: found 548 marked UTF-8 strings
Undeclared package ‘vcd’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
ConfA: no visible global function definition for ‘qf’
EstM2Sn: no visible global function definition for ‘nlm’
EstM2Sn: no visible global function definition for ‘qnorm’
TV.model: no visible global function definition for ‘dev.new’
TV.model: no visible global function definition for ‘points’
betaBino: no visible global function definition for ‘pbinom’
doseD: no visible global function definition for ‘lm’
doseD: no visible global function definition for ‘dev.new’
doseD: no visible global function definition for ‘par’
doseD: no visible global function definition for ‘axTicks’
doseD: no visible global function definition for ‘axis’
doseD: no visible global function definition for ‘lines’
doseD: no visible global function definition for ‘abline’
doseD: no visible global function definition for ‘legend’
setD: no visible global function definition for ‘dev.new’
setD: no visible global function definition for ‘par’
setD: no visible global function definition for ‘pbinom’
setD: no visible global function definition for ‘abline’
setD: no visible global function definition for ‘axis’
setD: no visible global function definition for ‘rect’
setD: no visible global function definition for ‘lines’
setD: no visible global function definition for ‘text’
setD: no visible global function definition for ‘axTicks’
setD: no visible global function definition for ‘legend’
spoD : spoD_A: no visible global function definition for ‘chisq.test’
Undefined global functions or variables:
  abline axTicks axis chisq.test dev.new legend lines lm nlm par pbinom
  points qf qnorm rect text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axTicks", "axis", "legend", "lines",
             "par", "points", "rect", "text")
  importFrom("stats", "chisq.test", "lm", "nlm", "pbinom", "qf", "qnorm")
to your NAMESPACE file.
Found the following files/directories:
  ‘01_spontaneous lethality.txt’ ‘02.sample size.txt’
  ‘03.dosestrategy.txt’ ‘doseD4.txt’ ‘setD.txt’ ‘spoDa.txt’ ‘spoDb.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘TPD-Ex.R’ failed
The error most likely occurred in:

> ### Name: REND
> ### Title: Functional Evenness, Richness and Divergence of Communities,
> ###   Species or Populations
> ### Aliases: REND
> 
> ### ** Examples
> 
> # 1.  Compute the TPDs of five different species. SP3 is in the center of
> #   the trait space, and the rest of species in the corners
> set.seed(1)
> species_ex <- c(rep("SP1",20), rep("SP2",20), rep("SP3",20), rep("SP4",20),
+              rep("SP5",20))
> traits_ex <- data.frame(trait1 = c(rnorm(20, 10, 1),
+                                    rnorm(20, 10, 1),
+                                    rnorm(20, 15, 1),
+                                    rnorm(20, 20, 1),
+                                    rnorm(20, 20, 1)),
+                         trait2 = c(rnorm(20, 10, 1),
+                                    rnorm(20, 20, 1),
+                                    rnorm(20, 15, 1),
+                                    rnorm(20, 10, 1),
+                                    rnorm(20, 20, 1)))
> species_TPDs <- TPDs (species = species_ex, traits = traits_ex)
-------Calculating densities for One population_Multiple species-----------

Error in t(x) - mean : non-numeric argument to binary operator
Calls: TPDs ... FUN -> kde.points -> dmvnorm.mixt -> dmvnorm -> backsolve
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘TPD.Rmd’ using rmarkdown
Quitting from lines 88-91 (TPD.Rmd) 
Error: processing vignette 'TPD.Rmd' failed with diagnostics:
non-numeric argument to binary operator
--- failed re-building ‘TPD.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 153 marked Latin-1 strings
  Note: found 108 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘rlang’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘V8’ ‘colorspace’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.7Mb
Undeclared packages ‘g.data’, ‘filehash’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘jpeg’ ‘pastecs’ ‘plyr’ ‘raster’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘suppdata’
  All declared Imports should be used.
Note: found 2 marked Latin-1 strings
  Note: found 701 marked UTF-8 strings
Package suggested but not available for checking: ‘taxidata’
'LazyData' is specified without a 'data' directory
Running examples in ‘TraMineRextras-Ex.R’ failed
The error most likely occurred in:

> ### Name: dissvar.grp
> ### Title: Discrepancy by group.
> ### Aliases: dissvar.grp
> ### Keywords: state sequences
> 
> ### ** Examples
> 
> ## create the biofam.seq state sequence object from the biofam data.
> data(biofam)
> biofam <- biofam[1:100,]
> biofam.seq <- seqdef(biofam[,10:25])
 [>] 6 distinct states appear in the data: 
     1 = 0
     2 = 1
     3 = 2
     4 = 3
     5 = 6
     6 = 7
 [>] state coding:
       [alphabet]  [label]  [long label] 
     1  0           0        0
     2  1           1        1
     3  2           2        2
     4  3           3        3
     5  6           6        6
     6  7           7        7
 [>] 100 sequences in the data set
 [>] min/max sequence length: 16/16
> dist <- seqdist(biofam.seq, method="HAM")
Error in dimnames(x) <- dn : 
  length of 'dimnames' [1] not equal to array extent
Calls: seqdist -> seqdur -> seqasnum -> rownames<-
Execution halted
Running examples in ‘TraMineR-Ex.R’ failed
The error most likely occurred in:

> ### Name: TraMineR-package
> ### Title: Trajectory Miner: a Toolbox for Exploring and Rendering
> ###   Sequences
> ### Aliases: TraMineR-package TraMineR
> ### Keywords: package
> 
> ### ** Examples
> 
> ## load the mvad data
> library(TraMineR)
> data(mvad)
> 
> ## create a state sequence object from columns 17 to 86
> mvad.seq <- seqdef(mvad[,17:86])
 [>] 6 distinct states appear in the data: 
     1 = FE
     2 = HE
     3 = employment
     4 = joblessness
     5 = school
     6 = training
 [>] state coding:
       [alphabet]  [label]     [long label] 
     1  FE          FE          FE
     2  HE          HE          HE
     3  employment  employment  employment
     4  joblessness joblessness joblessness
     5  school      school      school
     6  training    training    training
 [>] 712 sequences in the data set
 [>] min/max sequence length: 70/70
> 
> ## distribution plot by sex (male)
> seqdplot(mvad.seq, group=mvad$male, border=NA)
> 
> ## compute the LCS pairwise distance matrix
> ## among the first 10 sequences
> mvad.lcs <- seqdist(mvad.seq[1:10,], method="LCS")
Error in dimnames(x) <- dn : 
  length of 'dimnames' [1] not equal to array extent
Calls: seqdist -> seqdur -> seqasnum -> rownames<-
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘TraMineR-state-sequence.Rnw’ using Sweave

TraMineR stable version 2.2-2 (Built: 2021-12-02)
Website: http://traminer.unige.ch
Please type 'citation("TraMineR")' for citation information.

 [>] 6 distinct states appear in the data: 
     1 = FE
     2 = HE
     3 = employment
     4 = joblessness
     5 = school
     6 = training
 [>] state coding:
       [alphabet]  [label]     [long label] 
     1  employment  employment  employment
     2  FE          FE          FE
     3  HE          HE          HE
     4  joblessness joblessness joblessness
     5  school      school      school
     6  training    training    training
 [>] 712 sequences in the data set
 [>] min/max sequence length: 70/70

Error: processing vignette 'TraMineR-state-sequence.Rnw' failed with diagnostics:
 chunk 3 (label = mvad-dist) 
Error in dimnames(x) <- dn : 
  length of 'dimnames' [1] not equal to array extent

--- failed re-building 'TraMineR-state-sequence.Rnw'

SUMMARY: processing the following file failed:
  'TraMineR-state-sequence.Rnw'

Error: Vignette re-building failed.
Execution halted
installed size is 31.6Mb
  sub-directories of 1Mb or more:
    libs  29.6Mb
Running ‘AaregME.R’
  Running ‘LmME.R’
  Running ‘SurvregME.R’
  Running ‘basics.R’
  Running ‘methods.R’
  Running ‘predict.R’
  Running ‘simulate.R’
  Running ‘test_util.R’
  Running ‘tramTMB.R’
Running the tests in ‘tests/simulate.R’ failed.
Complete output:
  > ## -- Test utils & settings
  > source("test_util.R")
  > .run_test <- identical(Sys.getenv("NOT_CRAN"), "true")
  > oldopt <- options(digits = 4)
  > set.seed(100)
  > 
  > library("tramME")
  Loading required package: tram
  Loading required package: mlt
  Loading required package: basefun
  Loading required package: variables
  > data("sleepstudy", package = "lme4")
  > 
  > ## -- output structure
  > fit <- LmME(Reaction ~ Days + (Days | Subject), data = sleepstudy)
  > sim <- simulate(fit)
  > chkid(ifelse(is.numeric(sim), length(sim), nrow(sim)), nrow(sleepstudy))
  > sim <- simulate(fit, newdata = sleepstudy[1:4, ], nsim = 3)
  > chkid(length(sim), 3L)
  > chkid(ifelse(is.vector(sim[[1]]), length(sim[[1]]), nrow(sim[[1]])), 4L)
  > sim <- simulate(fit, ranef = ranef(fit, raw = TRUE), nsim = 2, bysim = FALSE)
  > chkid(length(sim), nrow(sleepstudy))
  > chkid(ifelse(is.vector(sim[[1]]), length(sim[[1]]), nrow(sim[[1]])), 2L)
  Error in chkid(ifelse(is.vector(sim[[1]]), length(sim[[1]]), nrow(sim[[1]])),  : 
    isTRUE(identical(x, y, ...)) is not TRUE
  Calls: chkid -> stopifnot
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
microsoftTranslate: no visible global function definition for
  ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
rtrapezoid: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Undeclared package ‘dplR’ in Rd xrefs
Running examples in ‘treecm-Ex.R’ failed
The error most likely occurred in:

> ### Name: anchorRange
> ### Title: Min/max values for the anchor position along the stem
> ### Aliases: anchorRange
> 
> ### ** Examples
> 
> library(treecm)
> data(stonePine1TreeData)
> vectors <- treeVectors(stonePine1TreeData)
Warning in `[.data.frame`(x$env$data, 1L, drop = FALSE) :
  'drop' argument will be ignored
Error in (function (azimuth, dBase, dTip, length, tipD, height, tilt,  : 
  argument "tipD" is missing, with no default
Calls: treeVectors ... loop_apply -> <Anonymous> -> .fun -> do.call -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘treecm.Rnw’ using Sweave
Warning in `[.data.frame`(x$env$data, 1L, drop = FALSE) :
  'drop' argument will be ignored

Error: processing vignette 'treecm.Rnw' failed with diagnostics:
 chunk 2 (label = ex11) 
Error in (function (azimuth, dBase, dTip, length, tipD, height, tilt,  : 
  argument "tipD" is missing, with no default

--- failed re-building ‘treecm.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘treedata.table-Ex.R’ failed
The error most likely occurred in:

> ### Name: extractVector
> ### Title: Returning a named vector from a treedata.table object
> ### Aliases: extractVector
> 
> ### ** Examples
> 
> 
> data(anolis)
> td <- as.treedata.table(tree = anolis$phy, data = anolis$dat)
Tip labels detected in column: trait
Phylo object detected 

No tips were dropped from the original tree/dataset
> # extracts the named vector for SVL from the td object
> extractVector(td, "SVL")
Error in names(object) <- nm : attempt to set an attribute on NULL
Calls: extractVector -> lapply -> FUN -> <Anonymous>
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(treedata.table)
  > 
  > test_check("treedata.table")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test.treedata.table.R:7:1): (code run outside of `test_that()`) ──────
  Error in `names(object) <- nm`: attempt to set an attribute on NULL
  Backtrace:
      █
   1. └─treedata.table::tdt(...) test.treedata.table.R:7:0
   2.   └─base::eval(call, env)
   3.     └─base::eval(call, env)
   4.       ├─geiger::fitContinuous(...)
   5.       │ └─geiger::treedata(phy, dat)
   6.       └─treedata.table::extractVector(td, "SVL")
   7.         └─base::lapply(vecs, function(x) stats::setNames(x, tdObject$phy$tip.label))
   8.           └─treedata.table:::FUN(X[[i]], ...)
   9.             └─stats::setNames(x, tdObject$phy$tip.label)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘AA_treedata.table_intro_english.Rmd’ using rmarkdown
Quitting from lines 56-58 (AA_treedata.table_intro_english.Rmd) 
Error: processing vignette 'AA_treedata.table_intro_english.Rmd' failed with diagnostics:
column(s) not found: SVL
--- failed re-building ‘AA_treedata.table_intro_english.Rmd’

--- re-building ‘AB_treedata.table_intro_spanish.Rmd’ using rmarkdown
Quitting from lines 55-57 (AB_treedata.table_intro_spanish.Rmd) 
Error: processing vignette 'AB_treedata.table_intro_spanish.Rmd' failed with diagnostics:
column(s) not found: SVL
--- failed re-building ‘AB_treedata.table_intro_spanish.Rmd’

--- re-building ‘B_multiphylo_treedata.table.Rmd’ using rmarkdown
Quitting from lines 56-57 (B_multiphylo_treedata.table.Rmd) 
Error: processing vignette 'B_multiphylo_treedata.table.Rmd' failed with diagnostics:
object 'ecomorph' not found
--- failed re-building ‘B_multiphylo_treedata.table.Rmd’

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

--- re-building ‘D_AdditionalFunctions_treedata.table.Rmd’ using rmarkdown
--- finished re-building ‘D_AdditionalFunctions_treedata.table.Rmd’

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

SUMMARY: processing the following files failed:
  ‘AA_treedata.table_intro_english.Rmd’
  ‘AB_treedata.table_intro_spanish.Rmd’
  ‘B_multiphylo_treedata.table.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘tree’
  All declared Imports should be used.
Package suggested but not available for checking: ‘TreeDistData’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
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.
Running examples in ‘treeman-Ex.R’ failed
The error most likely occurred in:

> ### Name: TreeMan-class
> ### Title: TreeMan-class
> ### Aliases: TreeMan-class TreeMan-method [[,TreeMan,character-method
> ###   [,TreeMan,character,missing,missing-method
> ###   as.character,TreeMan-method show,TreeMan-method print,TreeMan-method
> ###   str,TreeMan-method summary,TreeMan-method cTrees,TreeMan-method
> 
> ### ** Examples
> 
> library(treeman)
> # Generate random tree
> tree <- randTree(10)
> # Print to get basic stats
> summary(tree)
Tree (TreeMan Object):
  + 10 tips
  + 9 internal nodes
  + Binary
  + PD 8.33
  + Root node is "n1"
> # Slots....
> tree['tips']   # return all tips IDs
 [1] "t1"  "t10" "t2"  "t3"  "t4"  "t5"  "t6"  "t7"  "t8"  "t9" 
> tree['nds']    # return all internal node IDs
[1] "n1" "n2" "n3" "n4" "n5" "n6" "n7" "n8" "n9"
> tree['ntips']  # count all tips
[1] 10
> tree['nnds']   # count all internal nodes
[1] 9
> tree['root']   # identify root node
[1] "n1"
> tree[['t1']]   # return t1 node object
Node (tip node):
  + ID: "t1"
  + prid: "n5"
  + spn: 0.48
  + predist: 1.6
  + pd: 0
> tree['pd']     # return phylogenetic diversity
[1] 8.330796
> tree['ply']    # is polytomous?
[1] FALSE
> # Additional special slots (calculated upon call)
> tree['age']   # get tree's age
Warning in `[.data.frame`(x$env$data, 1L, drop = FALSE) :
  'drop' argument will be ignored
Error in ndlst[[id]] : no such index at level 2
Calls: [ ... .fun -> do.call -> <Anonymous> -> .getNdPridsFrmLst
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
LikAge: no visible global function definition for ‘read.table’
bd.ME.optim: no visible global function definition for ‘optim’
bd.ME.optim.rho: no visible global function definition for ‘optim’
bd.ME.optim.rho.all: no visible global function definition for ‘optim’
bd.MEyule.optim: no visible global function definition for ‘optimize’
bd.MEyule.optim: no visible global function definition for ‘optim’
bd.age.optim.matlab: no visible global function definition for
  ‘read.table’
bd.groups.conf: no visible global function definition for ‘uniroot’
bd.shifts.plot: no visible global function definition for ‘lines’
bdsky.stt.optim: no visible global function definition for ‘optim’
create.mat: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  lines optim optimize read.table uniroot write.table
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "optim", "optimize", "uniroot")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
plot.treeperm: no visible global function definition for ‘hist’
plot.treeperm: no visible global function definition for ‘points’
plot.treeperm: no visible global function definition for ‘text’
treeperm.formula: no visible global function definition for
  ‘model.frame’
treeperm.formula: no visible global function definition for
  ‘model.response’
Undefined global functions or variables:
  hist model.frame model.response points text
Consider adding
  importFrom("graphics", "hist", "points", "text")
  importFrom("stats", "model.frame", "model.response")
to your NAMESPACE file.
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 ‘treeplyr-Ex.R’ failed
The error most likely occurred in:

> ### Name: filter.treedata
> ### Title: Function for filtering rows from an object of class 'treedata'
> ### Aliases: filter.treedata filter.grouped_treedata
> 
> ### ** Examples
> 
> data(anolis)
> td <- make.treedata(anolis$phy, anolis$dat, name_column=1)
Error in dimnames(x) <- dn : 
  length of 'dimnames' [2] not equal to array extent
Calls: make.treedata -> colnames<-
Execution halted
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘boot’ ‘chron’ ‘randtoolbox’
  All declared Imports should be used.
installed size is 113.4Mb
  sub-directories of 1Mb or more:
    doc     3.8Mb
    libs  108.5Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  26.9Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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.
Namespace in Imports field not imported from: ‘gsrsb’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
cinbag: no visible global function definition for ‘var’
trimTrees: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict var
Consider adding
  importFrom("stats", "predict", "var")
to your NAMESPACE file.
File ‘trimTrees/libs/trimTrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘gtools’ ‘mgcv’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘gtools’ ‘mgcv’ ‘msm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HtoGp: no visible global function definition for ‘odd’
HtoGp: no visible global function definition for ‘even’
plot.pirls.gam: no visible global function definition for ‘par’
plot.pirls.gam: no visible global function definition for ‘title’
plot.pirls.gam: no visible global function definition for ‘lines’
plot.pirls.gam: no visible global function definition for ‘rug’
plot.pirls.gam: no visible global function definition for ‘mtext’
test.trioGxE: no visible global function definition for ‘write.table’
trioGxE: no visible global function definition for ‘quantile’
trioGxE: no visible global function definition for ‘qtnorm’
trioplot: no visible global function definition for ‘quantile’
trioplot: no visible global function definition for ‘formula’
trioplot: no visible global function definition for ‘gam’
trioplot: no visible global function definition for ‘binomial’
Undefined global functions or variables:
  binomial even formula gam lines mtext odd par qtnorm quantile rug
  title write.table
Consider adding
  importFrom("graphics", "lines", "mtext", "par", "rug", "title")
  importFrom("stats", "binomial", "formula", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Undeclared package ‘akima’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 118 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared package ‘SIBER’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
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').
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cdens: no visible global function definition for ‘head’
dplot: no visible global function definition for ‘knots’
dplot: no visible global function definition for ‘median’
dplot: no visible global function definition for ‘par’
dplot: no visible global function definition for ‘plot.stepfun’
dplot: no visible global function definition for ‘abline’
edf: no visible global function definition for ‘approxfun’
mctest : rdist: no visible global function definition for ‘runif’
mctest : S: no visible global function definition for ‘optim’
qplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline approxfun head knots median optim par plot.stepfun runif
Consider adding
  importFrom("graphics", "abline", "par")
  importFrom("stats", "approxfun", "knots", "median", "optim",
             "plot.stepfun", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
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.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ez’ ‘forcats’ ‘ggplot2’
  All declared Imports should be used.
Note: found 118 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tseries’
  All declared Imports should be used.
Undeclared packages ‘fpc’, ‘clValid’, ‘clv’ in Rd xrefs
tfDetails: no visible global function definition for ‘start’
tfDetails: no visible global function definition for ‘end’
Undefined global functions or variables:
  end start
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
Qhat: no visible global function definition for ‘pnorm’
plrt: no visible global function definition for ‘uniroot’
plrt: no visible global function definition for ‘optimize’
simulatedata: no visible global function definition for ‘rnorm’
tsc.test: no visible global function definition for ‘shapiro.test’
tsc.test: no visible global function definition for ‘p.adjust’
tsc.test: no visible global function definition for ‘glm’
tsc.test : f: no visible global function definition for ‘pnorm’
tsc.test: no visible global function definition for ‘uniroot’
tsc.test: no visible global function definition for ‘optimize’
variance: no visible global function definition for ‘density’
variance: no visible global function definition for ‘ecdf’
Undefined global functions or variables:
  density ecdf glm optimize p.adjust pnorm rnorm shapiro.test uniroot
Consider adding
  importFrom("stats", "density", "ecdf", "glm", "optimize", "p.adjust",
             "pnorm", "rnorm", "shapiro.test", "uniroot")
to your NAMESPACE file.
File ‘tsc/libs/tsc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘TSSQLite’, ‘TSMySQL’, ‘TSPostgreSQL’ in Rd xrefs
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   7.2Mb
Undeclared package ‘STPGA’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared package ‘rugarch’ in Rd xrefs
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘wordcloud2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  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.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tsibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘crosstalk’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
dLag : dlag.f: no visible global function definition for
  ‘complete.cases’
distmat: no visible global function definition for ‘dist’
fitCity: no visible global function definition for ‘glm.control’
fitCity: no visible global function definition for ‘terms’
ldmvnorm: no visible global function definition for ‘mahalanobis’
lspline: no visible global function definition for ‘quantile’
plot.tsdecomp: no visible global function definition for ‘par’
setupFormula: no visible global function definition for ‘as.formula’
spatialgibbs: no visible global function definition for ‘rnorm’
spatialgibbs: no visible global function definition for ‘rgamma’
spatialgibbs: no visible global function definition for ‘runif’
tsdecomp: no visible global function definition for ‘fft’
Undefined global functions or variables:
  as.formula complete.cases dist fft glm.control mahalanobis par
  quantile rgamma rnorm runif terms
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "as.formula", "complete.cases", "dist", "fft",
             "glm.control", "mahalanobis", "quantile", "rgamma", "rnorm",
             "runif", "terms")
to your NAMESPACE file.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Undeclared package ‘tseries’ in Rd xrefs
Malformed Title field: should not end in a period.
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.
'LazyData' is specified without a 'data' directory
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.
Namespaces in Imports field not imported from:
  ‘EMD’ ‘vars’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘gimms’ in Rd xrefs
Namespace in Imports field not imported from: ‘forecastHybrid’
  All declared Imports should be used.
Found the following files/directories:
  ‘XMIwords.txt’
Undeclared package ‘glmnet’ in Rd xrefs
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
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.
Namespace in Imports field not imported from: ‘latticeExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
.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.
Malformed Title field: should not end in a period.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Undeclared packages ‘multcomp’, ‘agricolae’ in Rd xrefs
Running examples in ‘TukeyC-Ex.R’ failed
The error most likely occurred in:

> ### Name: TukeyC
> ### Title: The TukeyC Test for Single Experiments
> ### Aliases: TukeyC TukeyC.default TukeyC.lm TukeyC.formula TukeyC.aovlist
> ###   TukeyC.lmerMod
> ### Keywords: package
> 
> ### ** Examples
> 
> ##
> ## Examples:Randomized Complete Block Design (RCBD)
> ## More details: demo(package='TukeyC')
> ##
> 
> ## The parameters can be: formula, aov, lm, aovlist and lmerMod
> 
> data(RCBD)
> 
> ## From: formula
> tk1 <- with(RCBD,
+             TukeyC(y ~ blk + tra,
+                    data=dfm,
+                    which='tra'))
Error in is.finite(x) : default method not implemented for type 'list'
Calls: with ... eval -> TukeyC -> TukeyC.formula -> TukeyC -> TukeyC.lm
Execution halted
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Undeclared package ‘randomForest’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Running examples in ‘tune-Ex.R’ failed
The error most likely occurred in:

> ### Name: conf_mat_resampled
> ### Title: Compute average confusion matrix across resamples
> ### Aliases: conf_mat_resampled
> 
> ### ** Examples
> 
> library(parsnip)
> library(rsample)
> library(dplyr)

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

> 
> data(two_class_dat, package = "modeldata")
> 
> set.seed(2393)
> res <-
+   logistic_reg() %>%
+   set_engine("glm") %>%
+   fit_resamples(Class ~ ., resamples = vfold_cv(two_class_dat, v = 3),
+                 control = control_resamples(save_pred = TRUE))
x Fold1: preprocessor 1/1, model 1/1: Error: `x` cannot be a vector.
x Fold2: preprocessor 1/1, model 1/1: Error: `x` cannot be a vector.
x Fold3: preprocessor 1/1, model 1/1: Error: `x` cannot be a vector.
Warning: All models failed. See the `.notes` column.
> 
> conf_mat_resampled(res)
Error: Cannot find the predicted classes. Was this a classification model?
Backtrace:
    █
 1. └─tune::conf_mat_resampled(res)
Execution halted
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.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Undeclared package ‘xgboost’ in Rd xrefs
Undeclared package ‘twang’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 34 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 9 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
TwoCop: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
File ‘TwoCop/libs/TwoCop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Crm: no visible global function definition for ‘integrate’
Crm : <anonymous>: no visible global function definition for
  ‘integrate’
Crm: no visible global function definition for ‘optimize’
ail1: no visible global function definition for ‘uniroot’
ail2 : fu : <anonymous>: no visible global function definition for
  ‘integrate’
ail2: no visible global function definition for ‘uniroot’
aip : fu : <anonymous>: no visible global function definition for
  ‘integrate’
aip: no visible global function definition for ‘uniroot’
ait1: no visible global function definition for ‘uniroot’
ait2 : fu : <anonymous>: no visible global function definition for
  ‘integrate’
ait2: no visible global function definition for ‘uniroot’
sim3p3: no visible global function definition for ‘rbinom’
simCrm: no visible global function definition for ‘rbinom’
simCrm: no visible global function definition for ‘palette’
simCrm: no visible global function definition for ‘gray’
simCrm: no visible global function definition for ‘abline’
simCrm: no visible global function definition for ‘lines’
ssim3p3: no visible global function definition for ‘txtProgressBar’
ssim3p3: no visible global function definition for ‘setTxtProgressBar’
ssimCrm: no visible global function definition for ‘txtProgressBar’
ssimCrm: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  abline gray integrate lines optimize palette rbinom setTxtProgressBar
  txtProgressBar uniroot
Consider adding
  importFrom("grDevices", "gray", "palette")
  importFrom("graphics", "abline", "lines")
  importFrom("stats", "integrate", "optimize", "rbinom", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc     7.1Mb
    ubinc   2.0Mb
installed size is 64.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs  61.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc        1.5Mb
    shinyapp   3.4Mb
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs       20.1Mb
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    help   3.6Mb
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.
Running examples in ‘unbalanced-Ex.R’ failed
The error most likely occurred in:

> ### Name: ubBalance
> ### Title: Balance wrapper
> ### Aliases: ubBalance
> 
> ### ** Examples
> 
> library(unbalanced)
> data(ubIonosphere)
> n<-ncol(ubIonosphere)
> output<-ubIonosphere$Class
> input<-ubIonosphere[ ,-n]
> 
> #balance the dataset
> data<-ubBalance(X= input, Y=output, type="ubSMOTE", percOver=300, percUnder=150, verbose=TRUE)
Error in ubSMOTE(X, Y, percOver, k, percUnder, verbose) : 
  X cannot be a vector
Calls: ubBalance -> ubSMOTE
Execution halted
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.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
Running examples in ‘ungroup-Ex.R’ failed
The error most likely occurred in:

> ### Name: pclm2D
> ### Title: Two-Dimensional Penalized Composite Link Model (PCLM-2D)
> ### Aliases: pclm2D
> 
> ### ** Examples
> 
> # Input data
> Dx <- ungroup.data$Dx
> Ex <- ungroup.data$Ex
> 
> # Aggregate data to be ungrouped in the examples below
> # Select a 10y data frame
> x      <- c(0, 1, seq(5, 85, by = 5))
> nlast  <- 26
> n      <- c(diff(x), nlast)
> group  <- rep(x, n)
> y      <- aggregate(Dx, by = list(group), FUN = "sum")[, 2:10]
> offset <- aggregate(Ex, by = list(group), FUN = "sum")[, 2:10]
> 
> # Example 1 ---------------------- 
> # Fit model and ungroup data using PCLM-2D
> P1 <- pclm2D(x, y, nlast)
   Ungrouping data      Error in diag(1, ncol = ny, nrow = ny) : 
  invalid 'nrow' value (too large or NA)
Calls: pclm2D ... with.default -> eval -> eval -> pclm.fit -> build_C_matrix -> diag
Execution halted
Running ‘testthat.R’ [14s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ungroup)
  > 
  > test_check("ungroup")
     Ungrouping data      ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • empty test (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_pclm2D.R:39:1): (code run outside of `test_that()`) ─────────────
  Error in `diag(1, ncol = ny, nrow = ny)`: invalid 'nrow' value (too large or NA)
  Backtrace:
      █
   1. └─ungroup::pclm2D(x, as.matrix(y2), nlast) test_pclm2D.R:39:0
   2.   ├─base::with(...)
   3.   └─base::with.default(...)
   4.     └─base::eval(substitute(expr), data, enclos = parent.frame())
   5.       └─base::eval(substitute(expr), data, enclos = parent.frame())
   6.         └─ungroup::pclm.fit(...)
   7.           └─ungroup::build_C_matrix(x, y, nlast, offset, out.step, type)
   8.             └─base::diag(1, ncol = ny, nrow = ny)
  
  [ FAIL 1 | WARN 1 | SKIP 1 | PASS 69 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘unifDAG-vignette.Rnw’ using knitr
Loading required package: knitr
Error: processing vignette 'unifDAG-vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'unifDAG-vignette.tex' failed.
LaTeX errors:
! Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
--- failed re-building ‘unifDAG-vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘unifDAG-vignette.Rnw’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
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.
Running examples in ‘unikn-Ex.R’ failed
The error most likely occurred in:

> ### Name: grepal
> ### Title: Get a vector of colors whose names match a regular expression.
> ### Aliases: grepal
> 
> ### ** Examples
> 
> grepal("cyan")
 [1] "cyan"       "cyan1"      "cyan2"      "cyan3"      "cyan4"     
 [6] "darkcyan"   "lightcyan"  "lightcyan1" "lightcyan2" "lightcyan3"
[11] "lightcyan4"
> 
> # With regular expressions:
> some_grey  <- grepal("gr(a|e)y")
> start_grey <- grepal("^gr(a|e)y")
> only_grey  <- grepal("^gr(a|e)y$")
> 
> length(some_grey)
[1] 224
> length(only_grey)
[1] 2
> 
> # With other color objects (df as x):
> grepal("blau", x = pal_unikn)
data frame with 0 columns and 1 row
> grepal("SEE", x = pal_unikn_pref)
data frame with 0 columns and 1 row
> 
> # Applications:
> seecol(grepal("white"), col_bg = "lightblue2", title = "See 'white' colors()")
> 
> olives  <- grepal("olive")
> oranges <- grepal("orange")
> seecol(list(olives, oranges), 
+        pal_names = c("olives", "oranges"), 
+        title = "Comparing olives and oranges")
> 
> seecol(grepal("SEE", pal_unikn), title = "All 'SEE' colors in pal_unikn")
Error in if (!pal %in% keys) { : argument is of length zero
Calls: seecol -> getpal_key
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘color_inst.Rmd’ using rmarkdown
Welcome to unikn (v0.4.0)!
unikn.guide() opens user guides.
--- finished re-building ‘color_inst.Rmd’

--- re-building ‘color_recipes.Rmd’ using rmarkdown
Quitting from lines 277-294 (color_recipes.Rmd) 
Error: processing vignette 'color_recipes.Rmd' failed with diagnostics:
attempt to set an attribute on NULL
--- failed re-building ‘color_recipes.Rmd’

--- re-building ‘colors.Rmd’ using rmarkdown
Quitting from lines 384-387 (colors.Rmd) 
Error: processing vignette 'colors.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘colors.Rmd’

--- re-building ‘text.Rmd’ using rmarkdown
Minimum y of layout is 0.05, while y_bot = 0.054
--- finished re-building ‘text.Rmd’

SUMMARY: processing the following files failed:
  ‘color_recipes.Rmd’ ‘colors.Rmd’

Error: Vignette re-building failed.
Execution halted
Note: found 548 marked UTF-8 strings
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘mirt’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘extraDistr’ ‘logitnorm’ ‘nakagami’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(universals)
  > 
  > test_check("universals")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-dims.R:22:3): dims.data.frame ─────────────────────────────────
  dims(data.frame()) not identical to c(0L, 0L).
  Lengths differ: 1 is not 2
  ── Failure (test-dims.R:23:3): dims.data.frame ─────────────────────────────────
  dims(data.frame(x = 2:3)) not identical to c(2L, 1L).
  Lengths differ: 1 is not 2
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 98 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is 29.4Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    1.6Mb
    libs  25.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 3345 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘lavaan’ ‘lifecycle’ ‘patchwork’ ‘ragg’ ‘scales’ ‘simstandard’
  All declared Imports should be used.
Running examples in ‘unusualprofile-Ex.R’ failed
The error most likely occurred in:

> ### Name: cond_maha
> ### Title: Calculate the conditional Mahalanobis distance for any
> ###   variables.
> ### Aliases: cond_maha
> 
> ### ** Examples
> 
> library(unusualprofile)
> library(simstandard)
> 
> m <- "
+ Gc =~ 0.85 * Gc1 + 0.68 * Gc2 + 0.8 * Gc3
+ Gf =~ 0.8 * Gf1 + 0.9 * Gf2 + 0.8 * Gf3
+ Gs =~ 0.7 * Gs1 + 0.8 * Gs2 + 0.8 * Gs3
+ Read =~ 0.66 * Read1 + 0.85 * Read2 + 0.91 * Read3
+ Math =~ 0.4 * Math1 + 0.9 * Math2 + 0.7 * Math3
+ Gc ~ 0.6 * Gf + 0.1 * Gs
+ Gf ~ 0.5 * Gs
+ Read ~ 0.4 * Gc + 0.1 * Gf
+ Math ~ 0.2 * Gc + 0.3 * Gf + 0.1 * Gs"
> # Generate 10 cases
> d_demo <- simstandard::sim_standardized(m = m, n = 10)
> 
> # Get model-implied correlation matrix
> R_all <- simstandard::sim_standardized_matrices(m)$Correlations$R_all
> 
> cond_maha(data = d_demo,
+           R = R_all,
+           v_dep = c("Math", "Read"),
+           v_ind = c("Gf", "Gs", "Gc"))
Error in data - colmu : non-numeric argument to binary operator
Calls: cond_maha
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(unusualprofile)
  > 
  > test_check("unusualprofile")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-main.R:36:3): Example works ─────────────────────────────────────
  Error in `data - colmu`: non-numeric argument to binary operator
  Backtrace:
      █
   1. ├─testthat::expect_silent(...) test-main.R:36:2
   2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
   3. │   ├─testthat:::.capture(...)
   4. │   │ ├─withr::with_output_sink(...)
   5. │   │ │ └─base::force(code)
   6. │   │ ├─base::withCallingHandlers(...)
   7. │   │ └─base::withVisible(code)
   8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   9. └─unusualprofile::cond_maha(data = d, R = R, v_dep = v_dep, v_ind_composites = v_ind_composites)
  ── Error (test-main.R:253:3): Metric does not matter ───────────────────────────
  Error in `data - colmu`: non-numeric argument to binary operator
  Backtrace:
      █
   1. ├─testthat::expect_equal(...) test-main.R:253:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─unusualprofile::cond_maha(data = d, R = R, v_dep = v_dep, v_ind_composites = v_ind_composites)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 23 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘tutorial_unusualprofile.Rmd’ using rmarkdown
Quitting from lines 431-596 (tutorial_unusualprofile.Rmd) 
Error: processing vignette 'tutorial_unusualprofile.Rmd' failed with diagnostics:
non-numeric argument to binary operator
--- failed re-building ‘tutorial_unusualprofile.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Note: found 7872 marked UTF-8 strings
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘ExtendedAppendix.Rnw’ using knitr
--- finished re-building ‘ExtendedAppendix.Rnw’

--- re-building ‘Manuscript.Rnw’ using knitr

Please cite as: 

 Hlavac, Marek (2018). stargazer: Well-Formatted Regression and Summary Statistics Tables.
 R package version 5.2.2. https://CRAN.R-project.org/package=stargazer 

Quitting from lines 545-549 (Manuscript.Rnw) 
Error: processing vignette 'Manuscript.Rnw' failed with diagnostics:
cannot coerce class 'c("glm", "lm")' to a data.frame
--- failed re-building ‘Manuscript.Rnw’

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

Error: Vignette re-building failed.
Execution halted
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.
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
Undeclared package ‘httr’ in Rd xrefs
Note: found 488 marked UTF-8 strings
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.
Undeclared package ‘sp’ in Rd xrefs
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘UScensus2000cdp/R/zzz.R’:
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000cdp\").\n")
    cat("Type help(package=\"UScensus2000cdp\") to get started.\n")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    data  26.4Mb
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'.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘cli’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘microservices’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tsibble’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   6.4Mb
Note: found 1 marked UTF-8 string
Note: found 33 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Undeclared package ‘dplyr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘stringdist’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'parallel' 'xml2'
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   8.7Mb
Namespace in Imports field not imported from: ‘Cairo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running examples in ‘validann-Ex.R’ failed
The error most likely occurred in:

> ### Name: ann
> ### Title: Fit Artificial Neural Networks.
> ### Aliases: ann
> 
> ### ** Examples
> 
> ## fit 1-hidden node ann model with tanh activation at the hidden layer and
> ## linear activation at the output layer.
> ## Use 200 random samples from ar9 dataset.
> ## ---
> data("ar9")
> samp <- sample(1:1000, 200)
> y <- ar9[samp, ncol(ar9)]
> x <- ar9[samp, -ncol(ar9)]
> x <- x[, c(1,4,9)]
> fit <- ann(x, y, size = 1, act_hid = "tanh", act_out = "linear", rang = 0.1)
Error in ann(x, y, size = 1, act_hid = "tanh", act_out = "linear", rang = 0.1) : 
  nrows of 'x' and 'y' must match
Execution halted
Namespaces in Imports field not imported from:
  ‘BBmisc’ ‘badger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘car’ ‘rlang’ ‘tidyverse’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      2.7Mb
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Mammen: no visible global function definition for ‘runif’
PR2: no visible global function definition for ‘ar.burg’
PR2: no visible global function definition for ‘pt’
PR2: no visible global function definition for ‘pf’
PR3: no visible global function definition for ‘ar.burg’
PR3: no visible global function definition for ‘pt’
PR3: no visible global function definition for ‘pf’
VAR.FOR: no visible global function definition for ‘qnorm’
VAR.ForeB: no visible global function definition for ‘runif’
VAR.LRtest: no visible global function definition for ‘pchisq’
VAR.LRtest: no visible global function definition for ‘pf’
VAR.PI: no visible global function definition for ‘quantile’
VAR.Waldtest: no visible global function definition for ‘pf’
VAR.irf: no visible global function definition for ‘par’
VAR.irf: no visible global function definition for ‘abline’
VAR1.sim: no visible global function definition for ‘rnorm’
resamp: no visible global function definition for ‘runif’
Undefined global functions or variables:
  abline ar.burg par pchisq pf pt qnorm quantile rnorm runif
Consider adding
  importFrom("graphics", "abline", "par")
  importFrom("stats", "ar.burg", "pchisq", "pf", "pt", "qnorm",
             "quantile", "rnorm", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘candisc’ in Rd xrefs
Found the following files/directories:
  ‘Output.txt’ ‘Overlap.csv’ ‘Polar coordinates.csv’
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
black_scholes: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Undeclared package ‘vars’ in Rd xrefs
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
burdenPlot: no visible global function definition for ‘density’
burdenPlot: no visible global function definition for ‘axis’
burdenPlot: no visible global function definition for ‘points’
burdenPlot: no visible global function definition for ‘lines’
burdenPlot: no visible global function definition for ‘abline’
burdenPlot: no visible global function definition for ‘text’
burdenPlot: no visible global function definition for ‘sd’
burdenPlot: no visible global function definition for ‘segments’
vbdm: no visible global function definition for ‘var’
vbdm: no visible global function definition for ‘pchisq’
vbdmR : run_discrete_mixture_vanilla: no visible global function
  definition for ‘var’
vbdmR: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  abline axis density lines pchisq points sd segments text var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "points", "segments",
             "text")
  importFrom("stats", "density", "pchisq", "sd", "var")
to your NAMESPACE file.
File ‘vbdm/libs/vbdm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
compute_KL : rtnorm: no visible global function definition for ‘runif’
compute_KL : rtnorm: no visible global function definition for ‘dnorm’
compute_KL: no visible global function definition for ‘qnorm’
compute_KL: no visible global function definition for ‘dnorm’
compute_KL: no visible global function definition for ‘pnorm’
compute_KL: no visible global function definition for ‘var’
compute_KL: no visible global function definition for ‘rbinom’
compute_KL: no visible global function definition for ‘rnorm’
compute_KL: no visible global function definition for ‘sd’
vbsr: no visible global function definition for ‘qchisq’
vbsr: no visible global function definition for ‘var’
vbsr: no visible global function definition for ‘pchisq’
vbsr: no visible global function definition for ‘sd’
vbsr: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  dnorm pchisq pnorm qchisq qnorm rbinom rnorm runif sd var
Consider adding
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qchisq", "qnorm",
             "rbinom", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
File ‘vbsr/libs/vbsr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘coin’, ‘Hmisc’ in Rd xrefs
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
'LazyData' is specified without a 'data' directory
Compare2FDS: no visible global function definition for ‘runif’
Compare2FDS: no visible global function definition for ‘lm’
Compare2FDS: no visible global function definition for ‘model.matrix’
Compare2FDS: no visible global function definition for ‘abline’
Compare2FDS: no visible global function definition for ‘lines’
Compare2FDS: no visible global function definition for ‘text’
Compare2Vdg: no visible global function definition for ‘par’
Compare2Vdg: no visible global function definition for ‘lines’
Compare2Vdg: no visible global function definition for ‘legend’
FDSPlot: no visible global function definition for ‘runif’
FDSPlot: no visible global function definition for ‘lm’
FDSPlot: no visible global function definition for ‘model.matrix’
FDSPlot: no visible global function definition for ‘abline’
Vdgraph: no visible global function definition for ‘par’
Vdgraph: no visible global function definition for ‘lines’
Vdgraph: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline legend lines lm model.matrix par runif text
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "text")
  importFrom("stats", "lm", "model.matrix", "runif")
to your NAMESPACE file.
File ‘Vdgraph/libs/Vdgraph.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
calculateParameters,AffineTransformation: no visible global function
  definition for ‘lm’
calculateParameters,AffineTransformation: no visible global function
  definition for ‘coef’
calculateParameters,SimilarityTransformation: no visible global
  function definition for ‘lm’
calculateParameters,SimilarityTransformation: no visible global
  function definition for ‘coef’
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for ‘points’
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for ‘legend’
Undefined global functions or variables:
  coef legend lm points
Consider adding
  importFrom("graphics", "legend", "points")
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘foreach’ ‘iterators’ ‘maps’ ‘spam’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘ade4’, ‘cclust’, ‘bipartite’, ‘labdsv’, ‘ellipse’, ‘vegan3d’, ‘coda’, ‘maptools’, ‘ape’, ‘picante’ in Rd xrefs
Undeclared package ‘vctrs’ in Rd xrefs
Undeclared packages ‘mclust’, ‘e1071’ in Rd xrefs
Error(s) in re-building vignettes:
--- re-building ‘VegetationClassification.Rnw’ using Sweave
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-7
--- finished re-building ‘VegetationClassification.Rnw’

--- re-building ‘MedRegExample.Rmd’ using rmarkdown
Quitting from lines 216-218 (MedRegExample.Rmd) 
Error: processing vignette 'MedRegExample.Rmd' failed with diagnostics:
unimplemented type 'list' in 'orderVector1'

--- failed re-building ‘MedRegExample.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Undeclared package ‘stringdist’ in Rd xrefs
Note: found 128 marked UTF-8 strings
Note: found 49 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Checking should be performed on sources prepared by ‘R CMD build’.
Non-standard file/directory found at top level:
  ‘src-java’
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.
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rapidoc’
  All declared Imports should be used.
Undeclared package ‘workflows’ in Rd xrefs
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    help   2.8Mb
Undeclared package ‘car’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Note: found 2 marked UTF-8 strings
Running examples in ‘VIC5-Ex.R’ failed
The error most likely occurred in:

> ### Name: print.vic_output
> ### Title: VIC model run for each gridcells
> ### Aliases: print.vic_output vic
> 
> ### ** Examples
> 
> # This is a sample data to run VIC.
> data(STEHE)
> 
> forcing <- STEHE$forcing
> soil <- STEHE$soil
> veg <- STEHE$veg
> 
> # Set the global options for a 7-days run.
> vic_param('start_year', 1949)
> vic_param('start_month', 1)
> vic_param('start_day', 1)
> vic_param('end_year', 1949)
> vic_param('end_month', 1)
> vic_param('end_day', 7)
> vic_param('step_per_day', 24)
> vic_param('snow_step_per_day', 24)
> vic_param('runoff_step_per_day', 24)
> 
> # Run VIC.
> outputs <- vic(forcing, soil, veg)
Error in vic(forcing, soil, veg) : 
  Columns of forcing data "PREC" (16) are too few for model require. It should no less than number of gridcells (54).
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(VIC5)
  > 
  > test_check("VIC5")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-vic.R:44:3): vic works ──────────────────────────────────────────
  Error in `vic(forcing, soil, veg, output_info = out_info)`: Columns of forcing data "PREC" (16) are too few for model require. It should no less than number of gridcells (54).
  Backtrace:
      █
   1. └─VIC5::vic(forcing, soil, veg, output_info = out_info) test-vic.R:44:2
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Note: found 60 marked UTF-8 strings
Note: found 468 marked UTF-8 strings
File ‘VIFCP/libs/VIFCP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
vif: no visible global function definition for ‘sd’
vif: no visible global function definition for ‘lm’
vif: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  lm pnorm sd
Consider adding
  importFrom("stats", "lm", "pnorm", "sd")
to your NAMESPACE file.
Rd file 'vif.Rd':
  \usage lines wider than 90 characters:
             vif(y, x, w0 = 0.05, dw = 0.05, subsize = 200, trace = TRUE, mode = c("dense", "sparse"))
  \examples lines wider than 100 characters:
             vif.sel <- vif(housingexp$y, housingexp$x, w0 = 0.0005, dw = 0.005, subsize = 300, trace = FALSE);

These lines will be truncated in the PDF manual.
Namespaces in Imports field not imported from:
  ‘mclust’ ‘rlang’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   3.1Mb
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Undeclared package ‘mi’ in Rd xrefs
Note: found 2754 marked UTF-8 strings
Running examples in ‘VIM-Ex.R’ failed
The error most likely occurred in:

> ### Name: mapMiss
> ### Title: Map with information about missing/imputed values
> ### Aliases: mapMiss
> ### Keywords: hplot
> 
> ### ** Examples
> 
> 
> data(chorizonDL, package = "VIM")
> data(kola.background, package = "VIM")
> coo <- chorizonDL[, c("XCOO", "YCOO")]
> ## for missing values
> x <- chorizonDL[, c("As", "Bi")]
> mapMiss(x, coo, kola.background)
Error in mapMiss(x, coo, kola.background) : 
  'x' and 'coords' must have equal number of elements/rows
Execution halted
'LazyData' is specified without a 'data' directory
Undeclared packages ‘foreach’, ‘copula’ in Rd xrefs
installed size is 44.5Mb
  sub-directories of 1Mb or more:
    libs  44.1Mb
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.
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
Undeclared packages ‘vioplot’, ‘beanplot’, ‘beeswarm’, ‘parviol’ in Rd xrefs
Package suggested but not available for checking: ‘fastshap’
Undeclared package ‘foreach’ in Rd xrefs
Unknown package ‘fastshap’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Running examples in ‘vip-Ex.R’ failed
The error most likely occurred in:

> ### Name: vi
> ### Title: Variable importance
> ### Aliases: vi vi.default vi.model_fit vi.WrappedModel vi.Learner
> 
> ### ** Examples
> 
> #
> # A projection pursuit regression example
> #
> 
> # Load the sample data
> data(mtcars)
> 
> # Fit a projection pursuit regression model
> mtcars.ppr <- ppr(mpg ~ ., data = mtcars, nterms = 1)
> 
> # Compute variable importance scores
> vi(mtcars.ppr, method = "firm", ice = TRUE)
Warning in `[.data.frame`(x$env$data, 1L, drop = FALSE) :
  'drop' argument will be ignored
Error in `[<-.data.frame`(`*tmp*`, , pred.var, value = list(cyl = c(4,  : 
  replacement element 1 has 3 rows, need 32
Calls: vi ... loop_apply -> <Anonymous> -> .fun -> [<- -> [<-.data.frame
Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   6.4Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘ggthemes’ ‘tibble’
  All declared Imports should be used.
installed size is 23.6Mb
  sub-directories of 1Mb or more:
    libs  22.9Mb
Namespace in Imports field not imported from: ‘sqldf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc           2.5Mb
    htmlwidgets   6.9Mb
Namespace in Imports field not imported from: ‘parcats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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:
  ‘RColorBrewer’ ‘colorspace’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘glue’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Decile.Plot: no visible global function definition for ‘barplot’
Decile.Plot: no visible global function definition for ‘axis’
Sliding.Window: no visible global function definition for ‘lines’
Sliding.Window: no visible global function definition for ‘legend’
Undefined global functions or variables:
  axis barplot legend lines
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Undeclared package ‘devtools’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is 72.7Mb
  sub-directories of 1Mb or more:
    libs  72.3Mb
Note: found 4954 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
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.
Namespace in Imports field not imported from: ‘glue’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘lme4’ in Rd xrefs
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   8.6Mb
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘misc3d’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Undeclared package ‘readr’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
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.
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘dftotable.Rmd’ using rmarkdown
--- finished re-building ‘dftotable.Rmd’

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

--- re-building ‘sumtable.Rmd’ using rmarkdown
Quitting from lines 271-278 (sumtable.Rmd) 
Error: processing vignette 'sumtable.Rmd' failed with diagnostics:
label vector must have as many elements as there are variables as will be in the sumtable. Use NA elements to fill in, or see help(sumtable) for other label formats that do not require every variable to have a label.
--- failed re-building ‘sumtable.Rmd’

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

--- re-building ‘vtablefunction.Rmd’ using rmarkdown
Quitting from lines 152-161 (vtablefunction.Rmd) 
Error: processing vignette 'vtablefunction.Rmd' failed with diagnostics:
label vector must have as many elements as there are variables in the data. Use NA elements to fill in, or see help(vtable) for other label formats that do not require every variable to have a label.
--- failed re-building ‘vtablefunction.Rmd’

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

SUMMARY: processing the following files failed:
  ‘sumtable.Rmd’ ‘vtablefunction.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘EnvStats’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘tibble’ in Rd xrefs
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.
Note: found 358074 marked UTF-8 strings
Undeclared package ‘RCurl’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is 69.6Mb
  sub-directories of 1Mb or more:
    libs  68.1Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘DT’ ‘ENMeval’ ‘RColorBrewer’ ‘dismo’ ‘dplyr’ ‘jsonlite’
  ‘leaflet.extras’ ‘raster’ ‘rgdal’ ‘rgeos’ ‘rmarkdown’ ‘shinyjs’
  ‘shinythemes’ ‘sp’ ‘spThin’ ‘spocc’ ‘zip’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘flextable’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   5.5Mb
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘washeR-Ex.R’ failed
The error most likely occurred in:

> ### Name: wash.out
> ### Title: Time Series Outlier Detection (washer)
> ### Aliases: wash.out
> 
> ### ** Examples
> 
> ## data without outliers but structured with co-movement between groups
> data("dati")
> ## first column for phenomenon
> ## 2° col for time written in ordered number or strings
> ## 3° col for group classification variable
> ## 4° col for values
> str(dati)
'data.frame':	800 obs. of  4 variables:
 $ phen : chr  "Temperature" "Temperature" "Temperature" "Temperature" ...
 $ time : int  1 1 1 1 1 1 1 1 1 1 ...
 $ zone : chr  "a01" "a02" "a03" "a04" ...
 $ value: num  2.43 20.39 25.26 7.07 16.04 ...
> ## 1° -> data.frame + no outlier
> out=wash.out(dati)
[1] "No linear analisys: too few data!"
> out
[1] 0
> length(out[,1])
Error in out[, 1] : incorrect number of dimensions
Execution halted
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘vctrs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘ReconstructedData.txt’ ‘ReconstructedDataStDev.txt’
  ‘ResampledReconstructions.txt’
  ‘ResampledReconstructionsStandardVariation.txt’
'LazyData' is specified without a 'data' directory
Running examples in ‘waves-Ex.R’ failed
The error most likely occurred in:

> ### Name: FilterSpectra
> ### Title: Filter spectral data frame based on Mahalanobis distance
> ### Aliases: FilterSpectra
> 
> ### ** Examples
> 
> library(magrittr)
> filtered.test <- ikeogu.2017 %>%
+   dplyr::select(-TCC) %>%
+   na.omit() %>%
+   FilterSpectra(df = .,
+                 filter = TRUE,
+                 return.distances = TRUE,
+                 num.col.before.spectra = 5,
+                 window.size = 15)
Error in FUN(x, aperm(array(STATS, dims[perm]), order(perm)), ...) : 
  non-numeric argument to binary operator
Calls: %>% -> FilterSpectra -> mahalanobis -> sweep
Execution halted
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.
'LazyData' is specified without a 'data' directory
Note: found 3133 marked UTF-8 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 4413 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
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.
Note: found 1537 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    client   9.6Mb
    doc      1.0Mb
'LazyData' is specified without a 'data' directory
File ‘webreadr/libs/webreadr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘shiny’ ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘here’ ‘rgeos’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running examples in ‘WeibullR-Ex.R’ failed
The error most likely occurred in:

> ### Name: BBB
> ### Title: Beta Binomial Bounds
> ### Aliases: BBB
> ### Keywords: regression reliability
> 
> ### ** Examples
> 
> set.seed(4321)
> obj<-wblr.fit(wblr(rweibull(10,1,1)))
Warning in xtfrm.data.frame(x) : cannot xtfrm data frames
Error in `[.data.frame`(x, order(x, na.last = na.last, decreasing = decreasing)) : 
  undefined columns selected
Calls: wblr.fit ... getPPP -> sort -> sort.default -> [ -> [.data.frame
Execution halted
Running examples in ‘WeightedCluster-Ex.R’ failed
The error most likely occurred in:

> ### Name: as.clustrange
> ### Title: Build a clustrange object to compare different clustering
> ###   solutions.
> ### Aliases: as.clustrange as.clustrange.twins as.clustrange.hclust
> ###   plot.clustrange as.clustrange.dtclust
> 
> ### ** Examples
> 
> data(mvad)
> ## Aggregating state sequence
> aggMvad <- wcAggregateCases(mvad[, 17:86], weights=mvad$weight)
> 
> ## Creating state sequence object
> mvad.seq <- seqdef(mvad[aggMvad$aggIndex, 17:86], weights=aggMvad$aggWeights)
 [>] 6 distinct states appear in the data: 
     1 = FE
     2 = HE
     3 = employment
     4 = joblessness
     5 = school
     6 = training
 [>] state coding:
       [alphabet]  [label]     [long label] 
     1  FE          FE          FE
     2  HE          HE          HE
     3  employment  employment  employment
     4  joblessness joblessness joblessness
     5  school      school      school
     6  training    training    training
 [>] sum of weights: 711.57 - min/max: 0.13/33.43
 [>] 490 sequences in the data set
 [>] min/max sequence length: 70/70
> 
> ## COmpute distance using Hamming distance
> diss <- seqdist(mvad.seq, method="HAM")
Error in dimnames(x) <- dn : 
  length of 'dimnames' [1] not equal to array extent
Calls: seqdist -> seqdur -> seqasnum -> rownames<-
Execution halted
Weighted.Box.test: no visible global function definition for ‘acf’
Weighted.Box.test: no visible binding for global variable ‘na.pass’
Weighted.Box.test: no visible global function definition for ‘pgamma’
Weighted.Box.test: no visible global function definition for ‘pchisq’
Weighted.LM.test: no visible global function definition for ‘acf’
Weighted.LM.test: no visible binding for global variable ‘na.pass’
Weighted.LM.test: no visible global function definition for ‘pgamma’
Undefined global functions or variables:
  acf na.pass pchisq pgamma
Consider adding
  importFrom("stats", "acf", "na.pass", "pchisq", "pgamma")
to your NAMESPACE file.
File ‘weightedScores/libs/weightedScores.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘slam’ in Rd xrefs
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 4102 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘foreign’ ‘grid’ ‘intergraph’ ‘lordif’ ‘survey’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gapminder’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Bundesliga.Mannschaft: no visible global function definition for ‘data’
Bundesliga.Mannschaft: no visible binding for global variable
  ‘Bundesliga’
Bundesliga.Tabelle: no visible global function definition for ‘data’
Bundesliga.Tabelle: no visible binding for global variable ‘Bundesliga’
Bundesliga.XML: no visible global function definition for ‘data’
Bundesliga.XML: no visible binding for global variable ‘Bundesliga’
sens.spec: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘wikibooks/R/Bundesliga.Mannschaft.R’:
  data(Bundesliga)
File ‘wikibooks/R/Bundesliga.Tabelle.R’:
  data(Bundesliga)
File ‘wikibooks/R/Bundesliga.XML.R’:
  data(Bundesliga)
See section ‘Good practice’ in ‘?data’.
Found the following files/directories:
  ‘Bundesliga.xml’ ‘myfile.xml’
'LazyData' is specified without a 'data' directory
Undeclared package ‘WikipediR’ in Rd xrefs
Undeclared package ‘httr’ in Rd xrefs
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.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘ggthemes’ ‘plotly’ ‘shinythemes’
  All declared Imports should be used.
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘drc’ ‘imputeTestbench’
  All declared Imports should be used.
Running examples in ‘windex-Ex.R’ failed
The error most likely occurred in:

> ### Name: plotTrait
> ### Title: Provides a visualisation of up to three-dimensional trait space
> ###   (not accounting for phylogeny) for data exploration
> ### Aliases: plotTrait
> 
> ### ** Examples
> 
> data(sample.data)
> plotTrait(sample.data,c("ou1","ou2"),focal=sample.data[,2])
Error in plotTrait(sample.data, c("ou1", "ou2"), focal = sample.data[,  : 
  Trait data must be numeric
Execution halted
Note: found 1 marked UTF-8 string
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.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
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.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
Running examples in ‘WMDB-Ex.R’ failed
The error most likely occurred in:

> ### Name: WMDB-package
> ### Title: Discriminant Analysis Methods by Weight Mahalanobis Distance and
> ###   bayes
> ### Aliases: WMDB-package WMDB
> ### Keywords: weighted Mahalanobis distance method,distance discriminant
> ###   analysis
> 
> ### ** Examples
> 
> ##all parameters equal
> X=iris[,1:4]
> G=gl(3,50)
> wmd(X,G,diag(rep(0.25,4)))
Warning in sweep(x, 2, center) :
  STATS does not recycle exactly across MARGIN
Error in x %*% cov : non-conformable arguments
Calls: wmd -> wmahalanobis -> diag
Execution halted
fit,Leader: no visible global function definition for ‘lm’
plotfit,Leader: no visible global function definition for ‘par’
Undefined global functions or variables:
  lm par
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "lm")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘Introductory-Econometrics-Examples.Rmd’ using rmarkdown

Please cite as: 

 Hlavac, Marek (2018). stargazer: Well-Formatted Regression and Summary Statistics Tables.
 R package version 5.2.2. https://CRAN.R-project.org/package=stargazer 

Quitting from lines 93-94 (Introductory-Econometrics-Examples.Rmd) 
Error: processing vignette 'Introductory-Econometrics-Examples.Rmd' failed with diagnostics:
cannot coerce class '"lm"' to a data.frame
--- failed re-building ‘Introductory-Econometrics-Examples.Rmd’

SUMMARY: processing the following file failed:
  ‘Introductory-Econometrics-Examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
Note: found 933 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Note: found 6738 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
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
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘evaluating-different-predictor-sets.Rmd’ using rmarkdown
Quitting from lines 89-127 (evaluating-different-predictor-sets.Rmd) 
Error: processing vignette 'evaluating-different-predictor-sets.Rmd' failed with diagnostics:
Can't subset columns that don't exist.
✖ Column `.config` doesn't exist.
--- failed re-building ‘evaluating-different-predictor-sets.Rmd’

SUMMARY: processing the following file failed:
  ‘evaluating-different-predictor-sets.Rmd’

Error: Vignette re-building failed.
Execution halted
Note: found 2 marked UTF-8 strings
Found the following files/directories:
  ‘aphiainfo.csv’ ‘tax.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Undeclared packages ‘wpp2010’, ‘wpp2012’ in Rd xrefs
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘fdadensity’ ‘locfit’ ‘locpol’ ‘modeest’
  All declared Imports should be used.
Running examples in ‘WRI-Ex.R’ failed
The error most likely occurred in:

> ### Name: confidenceBands
> ### Title: Confidence Bands for Wasserstein Regression
> ### Aliases: confidenceBands
> 
> ### ** Examples
> 
> alpha = 2
> beta = 1
> n = 50
> x1 = runif(n)
> t_vec = unique(c(seq(0, 0.05, 0.001), seq(0.05, 0.95, 0.05), seq(0.95, 1, 0.001)))
> set.seed(1)
> quan_obs = simulate_quantile_curves(x1, alpha, beta, t_vec)
> Xfit_df = data.frame(x1 = x1)
> res = wass_regress(rightside_formula = ~., Xfit_df = Xfit_df,
+                    Ytype = 'quantile', Ymat = quan_obs, Sup = t_vec)
> confidence_Band = confidenceBands(res, Xpred_df = data.frame(x1 = c(-0.5,0.5)),
+ type = 'both', fig_num = 2)
Error in confidenceBands(res, Xpred_df = data.frame(x1 = c(-0.5, 0.5)),  : 
  fig_num must be an positive integer less than nrow(Xpred_df)
Execution halted
Malformed Title field: should not end in a period.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       3.4Mb
    extdata   2.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File
  LICENCE
is not mentioned in the DESCRIPTION file.
'library' or 'require' call to ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
simul.wsvm: no visible binding for global variable ‘mixture.example’
Undefined global functions or variables:
  mixture.example
Rd file 'simul.wsvm.Rd':
  \usage lines wider than 90 characters:
         simul.wsvm(set.seeds = 123, obs.num = 1000, mu = c(0,0), cov.mat = 0.2*diag(2), X = NULL, Y = NULL)

Rd file 'wsvm.boost.Rd':
  \usage lines wider than 90 characters:
         wsvm.boost(X, Y, new.X, new.Y, c.n, B = 50, kernel.type = list(type = "rbf", par= 0.5), C = 4, eps = 1e-10, plotting = FALSE)

These lines will be truncated in the PDF manual.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   5.8Mb
Namespace in Imports field not imported from: ‘simts’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
File
  inst/LICENCE
will install at top-level and is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘CONTENTS’
Rd file 'classroom.Rd':
  \examples lines wider than 100 characters:
     {boxplot(classroom.first8$mathgain[classroom.first8$schoolid==i] ~ classroom.first8$classid[classroom.first8$schoolid==i],ylab="Mathgai ... [TRUNCATED]

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    bin   5.7Mb
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘RP2_data_1.txt’ ‘RP2_data_4.txt’ ‘RP2_qtl_1.txt’ ‘RP2_qtl_4.txt’
  ‘hp1_effect_qtl.txt’ ‘hp1_freq_mrk.txt’ ‘hp1_freq_qtl.txt’
  ‘hp1_genome.txt’ ‘hp1_last_hp_data.txt’ ‘hp1_lm_mrk.txt’
  ‘hp1_lm_qtl.txt’ ‘hp1_lm_qtl_mrk.txt’ ‘hp1_mrk.txt’ ‘hp1_qtl.txt’
  ‘hp2_effect_qtl.txt’ ‘hp2_freq_mrk.txt’ ‘hp2_freq_qtl.txt’
  ‘hp2_genome.txt’ ‘hp2_last_hp_data.txt’ ‘hp2_lm_mrk.txt’
  ‘hp2_lm_qtl.txt’ ‘hp2_lm_qtl_mrk.txt’ ‘hp2_mrk.txt’ ‘hp2_qtl.txt’
  ‘my_RP_data_1.txt’ ‘my_RP_data_4.txt’ ‘my_RP_mrk_1.txt’
  ‘my_RP_mrk_4.txt’
Undeclared package ‘RSiena’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘xgb.txt’
installed size is 32.5Mb
  sub-directories of 1Mb or more:
    libs  31.6Mb
GNU make is a SystemRequirements.
File
  LICENCE
is not mentioned in the DESCRIPTION file.
quadplot: no visible global function definition for ‘median’
xgobi: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  median write.table
Consider adding
  importFrom("stats", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
XHWE: no visible global function definition for ‘read.table’
result: no visible global function definition for ‘pchisq’
result: no visible global function definition for ‘rbinom’
result: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  pchisq rbinom read.table rmultinom
Consider adding
  importFrom("stats", "pchisq", "rbinom", "rmultinom")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘results.txt’
Namespace in Imports field not imported from: ‘psychTools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 36.5Mb
  sub-directories of 1Mb or more:
    java  34.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘rlang’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggdendro’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Undeclared package ‘readr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    libs  23.5Mb
'LazyData' is specified without a 'data' directory
Running examples in ‘xspliner-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot_model_comparison
> ### Title: Plot models comparison
> ### Aliases: plot_model_comparison
> 
> ### ** Examples
> 
> iris_data <- droplevels(iris[iris$Species != "setosa", ])
> library(e1071)
> library(randomForest)
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
> library(xspliner)
> # Build SVM model, random forest model and surrogate one constructed on top od SVM
> model_svm <- svm(Species ~  Sepal.Length + Sepal.Width + Petal.Length + Petal.Width,
+                  data = iris_data, probability = TRUE)
> model_rf <- randomForest(
+   Species ~  Sepal.Length + Sepal.Width + Petal.Length + Petal.Width,
+   data = iris_data
+ )
> model_xs <- xspline(
+   Species ~  xs(Sepal.Length) + xs(Sepal.Width) + xs(Petal.Length) + xs(Petal.Width),
+   model = model_svm
+ )
Warning in `[.data.frame`(x$env$data, 1L, drop = FALSE) :
  'drop' argument will be ignored
Error in `[<-.data.frame`(`*tmp*`, , pred.var, value = list(Sepal.Length = c(4.9,  : 
  replacement element 1 has 28 rows, need 100
Calls: xspline ... loop_apply -> <Anonymous> -> .fun -> [<- -> [<-.data.frame
Execution halted
'LazyData' is specified without a 'data' directory
Note: found 268 marked UTF-8 strings
Found the following files/directories:
  ‘xtable.html’ ‘xtable.tex’
Found the following files/directories:
  ‘OPT.csv’ ‘testTecan_defaultLiquid.csv’ ‘testTecan_setLiquid.csv’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    include   4.0Mb
    libs      1.5Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘RColorBrewer’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Non-standard file/directory found at top level:
  ‘CONTRIBUTORS’
'LazyData' is specified without a 'data' directory
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.
Malformed Title field: should not end in a period.
big.read.table: no visible global function definition for ‘read.table’
big.read.table: no visible global function definition for ‘object.size’
sparkline: no visible global function definition for ‘is.ts’
sparkline: no visible global function definition for ‘time’
sparkline: no visible global function definition for ‘boxplot’
Undefined global functions or variables:
  boxplot is.ts object.size read.table time
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "is.ts", "time")
  importFrom("utils", "object.size", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘CO2.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
Package in Depends field not imported from: ‘compiler’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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').
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
.NS.estimator: no visible global function definition for ‘lm’
.NS.estimator: no visible global function definition for ‘coef’
.NS.estimator: no visible global function definition for ‘na.omit’
.NS.estimator: no visible global function definition for ‘resid’
.NSS.estimator: no visible global function definition for ‘lm’
.NSS.estimator: no visible global function definition for ‘coef’
.NSS.estimator: no visible global function definition for ‘na.omit’
.NSS.estimator: no visible global function definition for ‘resid’
NSrates: no visible global function definition for ‘time’
Nelson.Siegel: no visible global function definition for ‘optimize’
Srates: no visible global function definition for ‘time’
Svensson: no visible global function definition for ‘median’
Svensson: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  coef lm median na.omit optimize resid time
Consider adding
  importFrom("stats", "coef", "lm", "median", "na.omit", "optimize",
             "resid", "time")
to your NAMESPACE file.
Rd file 'ECBYieldCurve.Rd':
  \examples lines wider than 100 characters:
     plot(mat.ECB, ECBYieldCurve[i,], type="o", xlab="Maturities structure in years", ylab="Interest rates values")

Rd file 'FedYieldCurve.Rd':
  \examples lines wider than 100 characters:
     plot(mat, FedYieldCurve[i,], type="o", xlab="Maturities structure in years", ylab="Interest rates values")

These lines will be truncated in the PDF manual.
kmeansN: no visible global function definition for ‘kmeans’
kmeansN: no visible global function definition for ‘aggregate’
kmeansN2: no visible global function definition for ‘aggregate’
kmeansN2: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  aggregate kmeans sd
Consider adding
  importFrom("stats", "aggregate", "kmeans", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘miniUI’ ‘shinyBS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 35.8Mb
  sub-directories of 1Mb or more:
    libs  35.4Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 34.8Mb
  sub-directories of 1Mb or more:
    libs  34.5Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘spelling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ghyp’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   3.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RNRCS’
'LazyData' is specified without a 'data' directory
Running examples in ‘zCompositions-Ex.R’ failed
The error most likely occurred in:

> ### Name: LPdata
> ### Title: La Paloma data set
> ### Aliases: LPdata
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(LPdata)
> 
> zPatterns(LPdata,label=0)
Error in zPatterns(LPdata, label = 0) : 
  X must be a matrix or data.frame class object
Execution halted
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘dplyr’ in Rd xrefs
Note: found 47 marked UTF-8 strings
Running examples in ‘ZIPBayes-Ex.R’ failed
The error most likely occurred in:

> ### Name: ZIPExt
> ### Title: Zero-inflated Poisson model under measurement error and external
> ###   validation data are available
> ### Aliases: ZIPExt
> ### Keywords: Core Main function
> 
> ### ** Examples
> 
> ## load data
> data(datasimExt)
> set.seed(0)
> example_ZIP_Ext <-  ZIPExt (Ystar = datasimExt$main$Ystar,
+                             Covarmainphi = datasimExt$main[,c("intercept","X1")],
+                             Covarmainmu = datasimExt$main[,c("intercept","X2")],
+                             Covarplus = datasimExt$main[,c("intercept","Zplus")],
+                             Covarminus = datasimExt$main[,c("intercept","Zminus")],
+                             Ystarval = datasimExt$validation$Ystar, 
+                             Yval = datasimExt$validation$Y,
+                             Covarvalplus = datasimExt$validation[,3:4],
+                             Covarvalminus = datasimExt$validation[,3:4],
+                             betaphi = c(0.7,-0.7), betamu = c(1,-1.5), 
+                             alphaplus = c(0,0), alphaminus=c(0,0),
+                             priorgamma = c(0.001,0.001), priormu = c(0,0),
+                             priorSigma = c(1,1), propsigmaphi = c(0.05,0.05), 
+                             nmcmc = 10) 
Error in as.matrix(Covarplusall) %*% t(t(alphaplus)) : 
  requires numeric/complex matrix/vector arguments
Calls: ZIPExt
Execution halted
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 146804 marked UTF-8 strings
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    libs  26.3Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
Undeclared package ‘loo’ in Rd xrefs
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘zdat’
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘SDMTools’
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘shinydashboard’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Non-standard file/directory found at top level:
  ‘doc’
Packages in Depends field not imported from:
  ‘Rglpk’ ‘corrplot’ ‘lattice’ ‘rgl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘abc-Ex.R’ failed
The error most likely occurred in:

> ### Name: cv4postpr
> ### Title: Leave-one-our cross validation for model selection ABC
> ### Aliases: cv4postpr
> ### Keywords: models htest
> 
> ### ** Examples
> 
> require(abc.data)
> data(human)
> ###Reduce the sample size of the simulations to reduce the running time.
> ###Do not do that with your own data!
> ss<-c(1:1000,50001:51000,100001:101000)
> cv.modsel <- cv4postpr(models[ss], stat.3pops.sim[ss,], nval=5, tols=c(.05,.1), method="rejection") 
Warning: No statistics names are given, using S1, S2, ...TRUE
Error in sumstat[mysamp, ] : subscript out of bounds
Calls: cv4postpr
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘abcvignette.Rnw’ using Sweave
Loading required package: abc.data
Loading required package: nnet
Loading required package: quantreg
Loading required package: SparseM

Attaching package: ‘SparseM’

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

    backsolve

Loading required package: MASS
Loading required package: locfit
locfit 1.5-9.4 	 2020-03-24
Warning: No statistics names are given, using S1, S2, ...TRUE

Error: processing vignette 'abcvignette.Rnw' failed with diagnostics:
 chunk 9 (label = modsel) 
Error in sumstat[mysamp, ] : subscript out of bounds

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

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

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘CVrej.ps’ ‘linhc.pdf’
Running examples in ‘abcrf-Ex.R’ failed
The error most likely occurred in:

> ### Name: covRegAbcrf
> ### Title: Predict posterior covariance between two parameters for new data
> ###   using two reg-ABC-RF objects
> ### Aliases: covRegAbcrf covRegAbcrf.regAbcrf
> 
> ### ** Examples
> 
> data(snp)
> modindex <- snp$modindex
> sumsta <- snp$sumsta[modindex == "3",]
> r <- snp$param$r[modindex == "3"]
> r <- r[1:500]
> sumsta <- sumsta[1:500,]
> data2 <- data.frame(r, sumsta)
> model.rf.r <- regAbcrf(r~., data2, ntree=100)
> N1 <- snp$param$N1[modindex == "3"]
> N1 <- N1[1:500]
> data3 <- data.frame(N1, sumsta) 
> model.rf.N1 <- regAbcrf(N1~., data3, ntree=100)
> data(snp.obs)
> covRegAbcrf(model.rf.r, model.rf.N1, snp.obs, 
+             data2, data3, ntree=100)
Error in predict.ranger.forest(forest, data, predict.all, num.trees, type,  : 
  Error: One or more independent variables not found in data.
Calls: covRegAbcrf ... predict -> predict.ranger -> predict -> predict.ranger.forest
Execution halted
'LazyData' is specified without a 'data' directory
multiplot: no visible global function definition for ‘rainbow’
multiplot: no visible global function definition for ‘text’
multiplot: no visible global function definition for ‘lines’
multiplot: no visible global function definition for ‘par’
plot.abf2: no visible global function definition for ‘abline’
plot.abf2: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline lines par rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "par", "text")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Found the following files/directories:
  ‘acceldata2.RData’
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.
'LazyData' is specified without a 'data' directory
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.
Malformed Description field: should contain one or more complete sentences.
print.funlinWLS: no visible global function definition for ‘pchisq’
print.linML: no visible global function definition for ‘pchisq’
print.loglinML: no visible global function definition for ‘pchisq’
print.satMarML: no visible global function definition for ‘pchisq’
print.satMcarWLS: no visible global function definition for ‘pchisq’
summary.funlinWLS: no visible global function definition for ‘pchisq’
summary.linML: no visible global function definition for ‘pchisq’
summary.loglinML: no visible global function definition for ‘pchisq’
summary.satMarML: no visible global function definition for ‘pchisq’
summary.satMcarWLS: no visible global function definition for ‘pchisq’
summary.waldTest: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Aggregate: no visible global function definition for ‘aggregate’
Aggregate: no visible binding for global variable ‘tail’
Aggregate: no visible binding for global variable ‘var’
cocktailEnsemble: no visible global function definition for ‘glm’
cocktailEnsemble: no visible global function definition for ‘binomial’
cocktailEnsemble: no visible global function definition for ‘step’
cocktailEnsemble: no visible binding for global variable ‘na.omit’
imputeMissings : <anonymous>: no visible global function definition for
  ‘median’
predict.cocktailEnsemble: no visible global function definition for
  ‘predict’
Undefined global functions or variables:
  aggregate binomial glm median na.omit predict step tail var
Consider adding
  importFrom("stats", "aggregate", "binomial", "glm", "median",
             "na.omit", "predict", "step", "var")
  importFrom("utils", "tail")
to your NAMESPACE file.
Rd file 'cocktailEnsemble.Rd':
  \examples lines wider than 100 characters:
     Credit <- data.frame(Credit[order(runif(nrow(Credit ))),])[1:100,c('V2','V3','V8','V11','V14','V15','Response')]

Rd file 'predict.cocktailEnsemble.Rd':
  \examples lines wider than 100 characters:
     Credit <- data.frame(Credit[order(runif(nrow(Credit ))),])[1:100,c('V2','V3','V8','V11','V14','V15','Response')]

These lines will be truncated in the PDF manual.
Namespace in Imports field not imported from: ‘hunspell’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
‘configure’: /bin/bash is not portable
Package suggested but not available for checking: ‘gWidgets2RGtk2’
Namespace in Imports field not imported from: ‘svglite’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 305 marked UTF-8 strings
Running examples in ‘act-Ex.R’ failed
The error most likely occurred in:

> ### Name: search_results_export
> ### Title: Exports search results
> ### Aliases: search_results_export
> 
> ### ** Examples
> 
> library(act)
> 
> # Search
> mysearch <- act::search_new(examplecorpus, pattern="yo")
> nrow(mysearch@results)
[1] 12
> 
> # Create temporary file path
> path <- tempfile(pattern = "searchresults", tmpdir = tempdir(),
+     			 fileext = ".xlsx")
> 
> # It makes more sense, however, to you define a destination folder
> # that is easier to access on your computer:
> ## Not run: 
> ##D 	path <- tempfile(pattern = "searchresults",
> ##D  					 tmpdir = "PATH_TO_AN_EXISTING_FOLDER_ON_YOUR_COMPUTER",
> ##D  					 fileext = ".xlsx")
> ## End(Not run)
> 
> # Save search results
> act::search_results_export(s=mysearch, path=path)
> 
> # Do your coding of the search results somewhere outside of act
> # ...
> 
> # Load search results
> mysearch.import <- act::search_results_import(path=path)
Error in act::search_results_import(path = path) : 
  Some necessary columns are missing in your input file'. Missing columns:  resultID transcript.name annotationID tier.name startSec endSec content content.norm hit hit.nr hit.length hit.pos.content hit.pos.fulltext search.mode hit.span
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Example.jpeg’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unknown package ‘AdaptFit’ in Rd xrefs
Depends: includes the non-default packages:
  'Matrix', 'coda', 'mvtnorm', 'MCMCpack', 'spatstat', 'parallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  ‘MCMCpack’ ‘Matrix’ ‘coda’ ‘mvtnorm’ ‘parallel’ ‘spatstat’
  Please remove these calls from your code.
Package in Depends field not imported from: ‘lattice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'getpar.Rd':
  \examples lines wider than 100 characters:
     ## Plot the conditional error function of the Lehmacher-Wassmer (1999) type that runs through (p1,p2)=(0.3,0.7)

Rd file 'parconv.Rd':
  \examples lines wider than 100 characters:
     ## Obtain the parameter c for Fisher's combination test, using the local level 0.05 for the test after the second stage

Rd file 'pathCEF.Rd':
  \examples lines wider than 100 characters:
     ## Compare the tests by Bauer and Koehne (1994), Lehmacher and Wassmer (1999) and Vandemeulebroecke (2006)

Rd file 'tsT.Rd':
  \examples lines wider than 100 characters:
     ## An example of non-uniqueness: the maximal alpha1 is returned; any smaller value would also be valid

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

> ### Name: adass.fr
> ### Title: Adaptive smoothing spline estimator for the function-on-function
> ###   linear regression model
> ### Aliases: adass.fr
> 
> ### ** Examples
> 
> library(adass)
> data<-simulate_data("Scenario HAT",n_obs=100)
Scenario HATError in t(x) - mean : non-numeric argument to binary operator
Calls: simulate_data -> beta -> <Anonymous> -> backsolve
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(adass)
  > 
  > test_check("adass")
  Scenario HAT══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-adass_functions.R:5:1): (code run outside of `test_that()`) ─────
  Error in `t(x) - mean`: non-numeric argument to binary operator
  Backtrace:
      █
   1. └─adass::simulate_data(case, n_obs = 100) test-adass_functions.R:5:0
   2.   └─adass:::beta(grid_s, grid_t)
   3.     └─mvtnorm::dmvnorm(...)
   4.       └─base::backsolve(dec, t(x) - mean, transpose = TRUE)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Benchmarking’
  All declared Imports should be used.
critical.values: no visible global function definition for ‘rnorm’
critical.values: no visible global function definition for ‘quantile’
mandel.test: no visible global function definition for ‘qf’
mtukey.test : p.test: no visible global function definition for ‘qf’
mtukey.test: no visible binding for global variable ‘quantile’
mtukey.test: no visible global function definition for ‘rnorm’
tukey.test: no visible global function definition for ‘qf’
Undefined global functions or variables:
  qf quantile rnorm
Consider adding
  importFrom("stats", "qf", "quantile", "rnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Running examples in ‘adea-Ex.R’ failed
The error most likely occurred in:

> ### Name: adea
> ### Title: ADEA analysis to variable selection in DEA
> ### Aliases: adea
> 
> ### ** Examples
> 
> data('cardealers4')
> input <- cardealers4[, 1:2]
> output <- cardealers4[, 3:4]
> 
> # Compute adea model
> model <- adea(input, output)
Error in lp_solve_dea(input = input, output = output, orientation = orientation,  : 
  input should be a numeric vector, a numeric matrix or a numeric dataframe.
Calls: adea -> lp_solve_dea
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘adea_load_leverage.Rmd’ using rmarkdown
Quitting from lines 43-46 (adea_load_leverage.Rmd) 
Error: processing vignette 'adea_load_leverage.Rmd' failed with diagnostics:
length of 'dimnames' [1] not equal to array extent
--- failed re-building ‘adea_load_leverage.Rmd’

--- re-building ‘adea_variable_selection.Rmd’ using rmarkdown
Quitting from lines 49-52 (adea_variable_selection.Rmd) 
Error: processing vignette 'adea_variable_selection.Rmd' failed with diagnostics:
input should be a numeric vector, a numeric matrix or a numeric dataframe.
--- failed re-building ‘adea_variable_selection.Rmd’

--- re-building ‘cadea.Rmd’ using rmarkdown
Quitting from lines 46-50 (cadea.Rmd) 
Error: processing vignette 'cadea.Rmd' failed with diagnostics:
length of 'dimnames' [1] not equal to array extent
--- failed re-building ‘cadea.Rmd’

SUMMARY: processing the following files failed:
  ‘adea_load_leverage.Rmd’ ‘adea_variable_selection.Rmd’ ‘cadea.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘filehash’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘parallel’ ‘rsvg’ ‘scales’
  All declared Imports should be used.
Found the following files/directories:
  ‘Bestmatches.csv’ ‘ID.csv’ ‘listsp.csv’ ‘mylabels.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘lifecycle’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘ads-Ex.R’ failed
The error most likely occurred in:

> ### Name: Couepia
> ### Title: Spatial pattern of Couepia caryophylloides in Paracou, a canopy
> ###   tree species of French Guiana.
> ### Aliases: Couepia
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Couepia)
> coca.spp <- spp(Couepia$trees, mark=Couepia$stage, window=Couepia$rect, triangles=Couepia$tri)
Error in swin(window, triangles) : is.numeric(triangles) is not TRUE
Calls: spp -> swin -> stopifnot
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘Hmisc’ ‘WRS2’ ‘boot’ ‘car’ ‘dplyr’ ‘effects’
  ‘effsize’ ‘forcats’ ‘ggplot2’ ‘lm.beta’ ‘nlme’ ‘readr’ ‘robust’
  ‘sandwich’ ‘sjstats’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘table_AeRobiology’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  ‘myplot.pdf’ ‘myplot.png’
File ‘ahaz/libs/ahaz.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mixexp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘randomNames’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘ans_19-2.jpg’ ‘display2d_19-2.jpg’ ‘dist(3)_19-2.jpg’
  ‘dist(4)_19-2.jpg’ ‘dist(mirror)_19-2.jpg’ ‘dist(mirror2)_19-2.jpg’
Namespaces in Imports field not imported from:
  ‘Rsolnp’ ‘SuperLearner’ ‘future.apply’ ‘ggplot2’ ‘progressr’ ‘stats’
  ‘utils’
  All declared Imports should be used.
Note: found 53 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 710 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 90 marked UTF-8 strings
Found the following files/directories:
  ‘stuve.pdf’
'LazyData' is specified without a 'data' directory
dke.fun.default: no visible global function definition for ‘hist’
kef: no visible global function definition for ‘dbinom’
kef: no visible global function definition for ‘dgamma’
kef: no visible global function definition for ‘dlnorm’
plot.dke.fun: no visible global function definition for ‘hist’
plot.dke.fun: no visible global function definition for ‘lines’
plot.hcvc.fun1d: no visible global function definition for
  ‘plot.default’
plot.hcvd.fun1d: no visible global function definition for
  ‘plot.default’
plot.kern.fun1d: no visible global function definition for
  ‘plot.default’
plot.kpmfe.fun1d: no visible global function definition for
  ‘plot.default’
plot.reg.fun1d: no visible global function definition for
  ‘plot.default’
simp_int: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dbinom dgamma dlnorm hist lines plot.default
Consider adding
  importFrom("graphics", "hist", "lines", "plot.default")
  importFrom("stats", "approx", "dbinom", "dgamma", "dlnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
akmeans: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  kmeans
Consider adding
  importFrom("stats", "kmeans")
to your NAMESPACE file.
adpbar: no visible global function definition for ‘optim’
alabama: no visible global function definition for ‘optim’
auglag: no visible global function definition for ‘modifyList’
auglag1: no visible global function definition for ‘optim’
auglag1: no visible global function definition for ‘nlminb’
auglag2: no visible global function definition for ‘optim’
auglag2: no visible global function definition for ‘nlminb’
auglag3: no visible global function definition for ‘optim’
auglag3: no visible global function definition for ‘nlminb’
augpen: no visible global function definition for ‘optim’
constrOptim.nl: no visible global function definition for ‘modifyList’
Undefined global functions or variables:
  modifyList nlminb optim
Consider adding
  importFrom("stats", "nlminb", "optim")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘taxize’
  All declared Imports should be used.
File ‘AlgDesign/libs/AlgDesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
batch.possSpells.fnc: no visible binding for global variable ‘words’
possSpells.fnc: no visible binding for global variable ‘len.phons’
possSpells.fnc: no visible binding for global variable ‘phon1’
possSpells.fnc: no visible binding for global variable ‘len.total’
possSpells.fnc: no visible binding for global variable ‘poss.spells’
Undefined global functions or variables:
  len.phons len.total phon1 poss.spells words
Found the following files/directories:
  ‘more.words.rda’ ‘more.words.txt’ ‘more.words_log.txt’
  ‘other.words.rda’ ‘other.words.txt’ ‘other.words_log.txt’
  ‘some.words.rda’ ‘some.words.txt’ ‘some.words_log.txt’
  ‘yet.more.words.rda’ ‘yet.more.words.txt’ ‘yet.more.words_log.txt’
'LazyData' is specified without a 'data' directory
Running examples in ‘alookr-Ex.R’ failed
The error most likely occurred in:

> ### Name: run_models
> ### Title: Fit binary classification model
> ### Aliases: run_models
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

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

    combine

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

    filter, lag

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

    intersect, setdiff, setequal, union

> 
> # Divide the train data set and the test data set.
> sb <- rpart::kyphosis %>%
+   split_by(Kyphosis)
> 
> # Extract the train data set from original data set.
> train <- sb %>%
+   extract_set(set = "train")
> 
> # Extract the test data set from original data set.
> test <- sb %>%
+   extract_set(set = "test")
> 
> # Sampling for unbalanced data set using SMOTE(synthetic minority over-sampling technique).
> train <- sb %>%
+   sampling_target(seed = 1234L, method = "ubSMOTE")
Error in unbalanced::ubSMOTE(data.frame(X), Y, perc.over = perc.over,  : 
  X cannot be a vector
Calls: %>% -> sampling_target -> <Anonymous>
Execution halted
'LazyData' is specified without a 'data' directory
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.
ahull_track: no visible global function definition for ‘psp’
ahull_track: no visible global function definition for ‘owin’
ahull_track: no visible global function definition for
  ‘runifpointOnLines’
dw_track: no visible global function definition for ‘psp’
dw_track: no visible global function definition for ‘owin’
dw_track: no visible global function definition for ‘runifpointOnLines’
Undefined global functions or variables:
  owin psp runifpointOnLines
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 171 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
EXP.step: no visible global function definition for ‘rgamma’
EXP.step: no visible global function definition for ‘rnorm’
MAX.step: no visible global function definition for ‘uniroot’
Norm.GMedian: no visible binding for global variable ‘median’
RNASeq.Data.Gene: no visible binding for global variable ‘quantile’
decom.initial: no visible global function definition for ‘kmeans’
decom.initial: no visible global function definition for ‘quantile’
decom.initial: no visible global function definition for ‘var’
dispersion.nb.QL: no visible binding for global variable ‘quantile’
est.mu.nb.mle: no visible global function definition for ‘runif’
est.v.nb.QL: no visible global function definition for ‘runif’
pdf2grid: no visible global function definition for ‘dnorm’
pdf2grid: no visible global function definition for ‘dgamma’
prior.grid: no visible global function definition for ‘sd’
prior.grid: no visible global function definition for ‘dnorm’
test.AMAP: no visible global function definition for ‘rgamma’
test.AMAP: no visible global function definition for ‘rnorm’
test.AMAP: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  dgamma dnorm kmeans median quantile rgamma rnorm runif sd uniroot var
Consider adding
  importFrom("stats", "dgamma", "dnorm", "kmeans", "median", "quantile",
             "rgamma", "rnorm", "runif", "sd", "uniroot", "var")
to your NAMESPACE file.
Rd file 'MGN.EM.Rd':
  \usage lines wider than 90 characters:
     MGN.EM(data, nK, p0 = NULL, d0 = 0, nK0 = 0, iter.max = 10, print.steps = FALSE, MGN0 = NULL, model = NULL, nMC = 10000)

Rd file 'test.AMAP.Rd':
  \usage lines wider than 90 characters:
     test.AMAP(data, MGN, del.lim = NULL, FC = NULL, print.steps = FALSE, Integration = "MC",nMC=NULL)
  \examples lines wider than 100 characters:
     data("SimuHapMap")  # a matrix 'counts' storing simulated data with 10000 genes, two treatments, of which each has 5 replicates

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘glue’ ‘promises’ ‘websocket’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
amltest: no visible global function definition for ‘var’
amltest: no visible global function definition for ‘optim’
amltest: no visible global function definition for ‘lm’
cleanclust: no visible global function definition for ‘cor’
cleanclust: no visible global function definition for ‘hclust’
cleanclust: no visible global function definition for ‘as.dist’
cleanclust: no visible global function definition for ‘cutree’
Undefined global functions or variables:
  as.dist cor cutree hclust lm optim var
Consider adding
  importFrom("stats", "as.dist", "cor", "cutree", "hclust", "lm",
             "optim", "var")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘dplyr’ ‘gridExtra’
  All declared Imports should be used.
AMOEBA : Classi: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘kernlab’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘SparkR’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘analyzer.Rmd’ using rmarkdown
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Quitting from lines 98-101 (analyzer.Rmd) 
Error: processing vignette 'analyzer.Rmd' failed with diagnostics:
undefined columns selected
--- failed re-building ‘analyzer.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Analyz.loadSteps,Analyz: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘BH-0.05-ListOfGenes.txt’ ‘BH-0.05-VM-ListOfGenes.txt’
  ‘CompleteListOfGenes.txt’ ‘GenesOutOfAnalysis.txt’
  ‘GenesOutOfAnalysis_NotEnoughObs.txt’
  ‘GenesOutOfAnalysis_NullVar.txt’ ‘VM-CompleteListOfGenes.txt’
  ‘bonferroni-0.05-ListOfGenes.txt’
  ‘bonferroni-0.05-VM-ListOfGenes.txt’
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.
Non-standard files/directories found at top level:
  ‘AnDE.pdf’ ‘DESCRIPTION.dcf’ ‘helpme’
Packages in Depends field not imported from:
  ‘discretization’ ‘foreign’ ‘functional’ ‘stringr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
aode: no visible global function definition for ‘Compose’
mdl: no visible global function definition for ‘cutPoints’
setVar: no visible global function definition for ‘Compose’
Undefined global functions or variables:
  Compose cutPoints
Malformed Description field: should contain one or more complete sentences.
andrews: no visible global function definition for ‘plot.new’
andrews: no visible global function definition for ‘plot.window’
andrews: no visible global function definition for ‘title’
andrews: no visible global function definition for ‘axis’
andrews: no visible global function definition for ‘box’
andrews: no visible global function definition for ‘lines’
andrews: no visible global function definition for ‘rainbow’
andrews: no visible global function definition for ‘hsv’
selectand: no visible global function definition for ‘lines’
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window rainbow title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "title")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tmg’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'library' or 'require' call to ‘tcltk’ which was already attached by Depends.
  Please remove these calls from your code.
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’
Undefined global functions or variables:
  flush.console read.table write.table
Consider adding
  importFrom("utils", "flush.console", "read.table", "write.table")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘car’ ‘datasets’ ‘dplyr’ ‘ggplot2’ ‘plotly’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mcclust’
  All declared Imports should be used.
aw_map: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘curl’ ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘boot’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
varbin: no visible global function definition for ‘boot’
Undefined global functions or variables:
  boot
Packages in Depends field not imported from:
  ‘boot’ ‘lme4’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘AER’ ‘ChainLadder’ ‘ISLR’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 230 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘APIS/libs/APIS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘yulab.utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘survival’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
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.
Non-standard file/directory found at top level:
  ‘apsrtable-Ex.R’
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following files/directories:
  ‘APBinary_PPV.csv’ ‘APBinary_TPF.csv’
  ‘APBinary_ap_summary(method=perturbation,B=1500).csv’
  ‘APBinary_auc_summary(method=perturbation,B=1500).csv’
  ‘APSurv_PPV.csv’ ‘APSurv_TPF.csv’
  ‘APSurv_ap_summary(method=bootstrap,B=500).csv’
  ‘APSurv_auc_summary(method=bootstrap,B=500).csv’
  ‘CompareAP_Binary_dap_summary(method=none).csv’
  ‘CompareAP_Survival_dap_summary(method=bootstrap,B=500).csv’
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggthemes’ ‘shinythemes’ ‘tibble’
  All declared Imports should be used.
Note: found 76 marked Latin-1 strings
Namespaces in Imports field not imported from:
  ‘bannerCommenter’ ‘config’ ‘feather’ ‘here’ ‘knitr’ ‘log4r’ ‘ps’
  ‘rmarkdown’ ‘skimr’ ‘snakecase’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
ardec: no visible global function definition for ‘filter’
ardec.lm: no visible global function definition for ‘ar’
ardec.lm: no visible global function definition for ‘lm’
Undefined global functions or variables:
  ar filter lm
Consider adding
  importFrom("stats", "ar", "filter", "lm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Running examples in ‘areaplot-Ex.R’ failed
The error most likely occurred in:

> ### Name: confplot
> ### Title: Plot Confidence Bands
> ### Aliases: confplot confplot.default confplot.formula
> 
> ### ** Examples
> 
> model <- lm(log(dist)~log(speed), cars)
> ci95 <- predict(model, data.frame(speed=4:25), interval="confidence")
> ci50 <- predict(model, data.frame(speed=4:25), interval="confidence", level=0.5)
> x <- log(4:25)
> y1 <- ci95[,"lwr"]
> y2 <- ci95[,"upr"]
> mydata <- data.frame(x, y1, y2)
> 
> # Input format
> confplot(x, y1, y2)               # vectors
> confplot(x, cbind(y1,y2))         # y values in 2 columns
> confplot(mydata)                  # data in 3 columns
Error in confplot.default(mydata) : 
  'y1' should not be NULL when 'x' is a vector
Calls: confplot -> confplot.default
Execution halted
Namespaces in Imports field not imported from:
  ‘purrr’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Rd file 'sdafilter.Rd':
  \examples lines wider than 100 characters:
     plot(lon,lat,col="lightgrey",type="l",xlim=c(5,18), ylim=c(77.1,79.1),xlab="Longitude",ylab="Latitude")

Rd file 'vmask.Rd':
  \examples lines wider than 100 characters:
     plot(lon,lat,col="lightgrey",type="l",xlim=c(5,18), ylim=c(77.1,79.1),xlab="Longitude",ylab="Latitude")

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MonetDBLite’
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘gmm’ ‘graphics’ ‘sandwich’ ‘stats4’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘ARTP’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MSToutput.txt’
ASP.Score: no visible global function definition for ‘pnorm’
Graphs.Bayesian: no visible global function definition for ‘dev.new’
colorhex: no visible global function definition for ‘gray’
colorhex: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  dev.new gray pnorm rgb
Consider adding
  importFrom("grDevices", "dev.new", "gray", "rgb")
  importFrom("stats", "pnorm")
to your NAMESPACE file.
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.
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘arules’ ‘arulesViz’ ‘dplyr’ ‘methods’ ‘plotly’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
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.
CALPHA: no visible global function definition for ‘dbinom’
CALPHA: no visible global function definition for ‘pchisq’
CAST: no visible global function definition for ‘fisher.test’
CAST: no visible global function definition for ‘chisq.test’
CMC: no visible global function definition for ‘pf’
MULTI: no visible global function definition for ‘complete.cases’
RVT1: no visible global function definition for ‘pchisq’
RVT2: no visible global function definition for ‘pchisq’
RWAS: no visible global function definition for ‘pnorm’
SKAT: no visible global function definition for ‘dbeta’
SKAT: no visible global function definition for ‘pchisq’
TTEST: no visible global function definition for ‘complete.cases’
TTEST: no visible global function definition for ‘pf’
WST: no visible global function definition for ‘mvfft’
WST: no visible global function definition for ‘pnorm’
my_cmc_method: no visible global function definition for
  ‘complete.cases’
my_getUV: no visible global function definition for ‘complete.cases’
my_orwss_method: no visible global function definition for ‘sd’
my_rarecov_method: no visible global function definition for
  ‘chisq.test’
my_rbt_method: no visible global function definition for ‘ppois’
my_score_method: no visible global function definition for ‘pchisq’
my_ssu_method: no visible global function definition for ‘pchisq’
my_ssuw_method: no visible global function definition for ‘pchisq’
my_sum_method: no visible global function definition for ‘pchisq’
my_uminp_method: no visible global function definition for ‘pchisq’
my_uminp_method: no visible global function definition for ‘pmvnorm’
Undefined global functions or variables:
  chisq.test complete.cases dbeta dbinom fisher.test mvfft pchisq pf
  pmvnorm pnorm ppois sd
Consider adding
  importFrom("stats", "chisq.test", "complete.cases", "dbeta", "dbinom",
             "fisher.test", "mvfft", "pchisq", "pf", "pnorm", "ppois",
             "sd")
to your NAMESPACE file.
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.
Package suggested but not available for checking: ‘asteRiskData’
beamDiskOverlap: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
fm_unred: no visible global function definition for ‘spline’
galage: no visible global function definition for ‘integrate’
lumdist: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate spline
Consider adding
  importFrom("stats", "integrate", "spline")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
VPC.graph : findQuantile: no visible global function definition for
  ‘quantile’
VPC.graph : findQuantileCI : <anonymous>: no visible global function
  definition for ‘quantile’
asVPC.binW: no visible global function definition for ‘median’
asVPC.binW : <anonymous>: no visible global function definition for
  ‘quantile’
asVPC.binW: no visible global function definition for ‘quantile’
asVPC.distanceW: no visible global function definition for ‘median’
asVPC.distanceW : <anonymous>: no visible global function definition
  for ‘quantile’
asVPC.distanceW: no visible global function definition for ‘quantile’
makeCOVbin: no visible global function definition for ‘quantile’
makeCOVbin: no visible global function definition for ‘median’
read_Simdata: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  median quantile read.table
Consider adding
  importFrom("stats", "median", "quantile")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
get.est.ATT: no visible global function definition for ‘tail’
get.est.MT: no visible global function definition for ‘tail’
get.est.simple: no visible global function definition for ‘tail’
newton.r: no visible global function definition for ‘tail’
plot.ATE: no visible global function definition for ‘par’
plot.ATE: no visible global function definition for ‘axis’
plot.ATE: no visible global function definition for ‘abline’
plot.ATE: no visible global function definition for ‘lines’
plot.ATE: no visible global function definition for ‘legend’
plot.ATE: no visible global function definition for ‘points’
print.summary.ATE: no visible global function definition for
  ‘printCoefmat’
summary.ATE: no visible global function definition for ‘qnorm’
summary.ATE: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline axis legend lines par pnorm points printCoefmat qnorm tail
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "points")
  importFrom("stats", "pnorm", "printCoefmat", "qnorm")
  importFrom("utils", "tail")
to your NAMESPACE file.
Running examples in ‘ATE-Ex.R’ failed
The error most likely occurred in:

> ### Name: Cressie and Read objective functions
> ### Title: Cressie and Read objective functions
> ### Aliases: 'Cressie and Read function' cr.rho d.cr.rho dd.cr.rho
> 
> ### ** Examples
> 
> #Cressie-Read Family example
> data("nsw")
> Y<-nsw$re78[301:500]
> X<-nsw[301:500,-c(1,9)]
> treat<-nsw$treat[301:500]
> 
> #Exponential tilting
> ATE(Y,treat,X,theta = 0)
Warning in ATE(Y, treat, X, theta = 0) :
  Data matrix 'X' is a vector, will be treated as n x 1 matrix
Error in ATE(Y, treat, X, theta = 0) : 
  Dimensions of covariates and response do not match
Execution halted
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘lubridate’ ‘openair’ ‘plotly’
  All declared Imports should be used.
atmcmc : rmvtnorm: no visible global function definition for ‘rnorm’
atmcmc: no visible global function definition for ‘rnorm’
atmcmc: no visible global function definition for ‘runif’
atmcmc: no visible global function definition for ‘par’
atmcmc: no visible global function definition for ‘lm’
atmcmc: no visible global function definition for ‘lines’
atmcmc: no visible global function definition for ‘var’
atmcmc: no visible global function definition for ‘cov’
atmcmc: no visible global function definition for ‘quantile’
atmcmc: no visible global function definition for ‘sd’
plotmcmc: no visible global function definition for ‘pdf’
plotmcmc: no visible global function definition for ‘par’
plotmcmc: no visible global function definition for ‘dev.new’
plotmcmc: no visible global function definition for ‘png’
plotmcmc: no visible global function definition for ‘hist’
plotmcmc: no visible global function definition for ‘dev.off’
plotmcmc: no visible global function definition for ‘lines’
Undefined global functions or variables:
  cov dev.new dev.off hist lines lm par pdf png quantile rnorm runif sd
  var
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf", "png")
  importFrom("graphics", "hist", "lines", "par")
  importFrom("stats", "cov", "lm", "quantile", "rnorm", "runif", "sd",
             "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
PlotAtm.lin : scale_image: no visible global function definition for
  ‘heat.colors’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘par’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘sd’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘approx’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘image’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘axis’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘mtext’
PlotAtm.lin: no visible global function definition for ‘arrows’
PlotAtm.lin: no visible global function definition for ‘text’
PlotAtm.lin: no visible global function definition for ‘polygon’
sky.colors: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  approx arrows axis heat.colors image mtext par polygon rgb sd text
Consider adding
  importFrom("grDevices", "heat.colors", "rgb")
  importFrom("graphics", "arrows", "axis", "image", "mtext", "par",
             "polygon", "text")
  importFrom("stats", "approx", "sd")
to your NAMESPACE file.
Rd file 'MakeArrivals.lin.Rd':
  \examples lines wider than 100 characters:
     MakeArrivals.lin(xs = c(100, 150), ys = c(100, 150), zs = c(100, 150), xr = 0, yr = 0, zr = 0, dt = 0.01, nt = 100, timing = c(0, 0), A ... [TRUNCATED]

Rd file 'MakeAtmList.lin.Rd':
  \usage lines wider than 90 characters:
     MakeAtmList.lin(z0 = 0, c0 = 343, gc = 0, wx0 = 0, gwx = 0, wy0 = 0, gwy = 0, rho0 = 1.2929 * exp(-z0/6800), grho = -0.0001901323 * exp ... [TRUNCATED]

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dlnm’ ‘ggplot2’ ‘lubridate’ ‘mvmeta’ ‘pbs’ ‘tsModel’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
plot.AUC: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines
Consider adding
  importFrom("graphics", "lines")
to your NAMESPACE file.
AUCRFcv: no visible global function definition for ‘predict’
plot.AUCRF: no visible global function definition for ‘par’
plot.AUCRF: no visible global function definition for ‘dotchart’
plot.AUCRF: no visible global function definition for ‘title’
plot.AUCRF: no visible global function definition for ‘text’
Undefined global functions or variables:
  dotchart par predict text title
Consider adding
  importFrom("graphics", "dotchart", "par", "text", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘RJSONIO’ ‘hexbin’ ‘plotrix’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
audioHist: no visible global function definition for ‘hist’
audioHist: no visible global function definition for ‘rescale’
audioHist: no visible global function definition for ‘toJSON’
audioScatter: no visible binding for global variable ‘formula’
audioScatter: no visible global function definition for ‘hexbinplot’
audioScatter: no visible global function definition for ‘cor’
audioScatter: no visible global function definition for ‘toJSON’
audioSplom: no visible global function definition for ‘hexplom’
audioSplom: no visible binding for global variable ‘BTY’
audioSplom: no visible binding for global variable ‘panel.hexboxplot’
audioSplom: no visible global function definition for ‘combn’
audioSplom : <anonymous>: no visible global function definition for
  ‘cor’
audioSplom : <anonymous>: no visible global function definition for
  ‘toJSON’
audiolyzRcheck: no visible global function definition for
  ‘download.file’
audiolyzRcheck: no visible global function definition for ‘unzip’
matricize: no visible global function definition for ‘hexbin’
panel.audiolyzR: no visible global function definition for
  ‘panel.hexbinplot’
Undefined global functions or variables:
  BTY combn cor download.file formula hexbin hexbinplot hexplom hist
  panel.hexbinplot panel.hexboxplot rescale toJSON unzip
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "cor", "formula")
  importFrom("utils", "combn", "download.file", "unzip")
to your NAMESPACE file.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 552 marked UTF-8 strings
Package which this enhances but not available for checking: ‘rPython’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘broom’ ‘diptest’ ‘ggplot2’ ‘hexbin’ ‘moments’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘broom’ ‘tibble’ ‘usethis’
  All declared Imports should be used.
Running examples in ‘autoimage-Ex.R’ failed
The error most likely occurred in:

> ### Name: autopoints
> ### Title: Automatic facetting of multiple projected scatterplots
> ### Aliases: autopoints
> 
> ### ** Examples
> 
> data(co, package = "gear")
> easting = co$easting
> northing = co$northing
> # heated scatterplot for Aluminum and Cadmium
> autopoints(easting, northing, co[,c("Al", "Ca")],
+            common.legend = FALSE, map = "state",
+            main = c("Al", "Ca"), lratio = 0.2,
+            legend.mar = c(0.3, 0.1, 0.1, 0.1))
Error in autopoints_xyz_setup(x, y, z, tx = deparse(substitute(x)), ty = deparse(substitute(y)),  : 
  length(z) must equal length(x) when z is a vector
Calls: autopoints -> autopoints_xyz_setup
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘autoimage.Rmd’ using rmarkdown
--- finished re-building ‘autoimage.Rmd’

--- re-building ‘autopoints.Rmd’ using rmarkdown
Quitting from lines 59-62 (autopoints.Rmd) 
Error: processing vignette 'autopoints.Rmd' failed with diagnostics:
length(z) must equal length(x) when z is a vector
--- failed re-building ‘autopoints.Rmd’

--- re-building ‘ggplot2-comparison.Rmd’ using rmarkdown
--- finished re-building ‘ggplot2-comparison.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'library' or 'require' calls in package code:
  ‘ggplot2’ ‘gpclib’ ‘maptools’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
gLog.ep: no visible global function definition for ‘quantile’
gedestp: no visible global function definition for ‘na.omit’
gedestp: no visible global function definition for ‘optim’
gets.mean: no visible global function definition for ‘start’
gets.mean: no visible global function definition for ‘end’
gets.mean: no visible global function definition for ‘window’
gets.mean: no visible global function definition for ‘pt’
gets.mean: no visible global function definition for ‘Box.test’
gets.mean: no visible global function definition for ‘pchisq’
gets.vol: no visible global function definition for ‘start’
gets.vol: no visible global function definition for ‘end’
gets.vol: no visible global function definition for ‘window’
gets.vol: no visible global function definition for ‘pt’
gets.vol: no visible global function definition for ‘Box.test’
gets.vol: no visible global function definition for ‘pchisq’
jb.test: no visible global function definition for ‘pchisq’
skewness.test: no visible global function definition for ‘pchisq’
sm: no visible global function definition for ‘start’
sm: no visible global function definition for ‘end’
sm: no visible global function definition for ‘window’
sm: no visible global function definition for ‘pt’
sm: no visible global function definition for ‘pchisq’
sm: no visible global function definition for ‘Box.test’
Undefined global functions or variables:
  Box.test end na.omit optim pchisq pt quantile start window
Consider adding
  importFrom("stats", "Box.test", "end", "na.omit", "optim", "pchisq",
             "pt", "quantile", "start", "window")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BBmisc’ ‘Ckmeans.1d.dp’ ‘Matrix’ ‘broom.mixed’ ‘ggstance’ ‘glmnet’
  All declared Imports should be used.
Running examples in ‘autostats-Ex.R’ failed
The error most likely occurred in:

> ### Name: auto_variable_contributions
> ### Title: Plot Variable Contributions
> ### Aliases: auto_variable_contributions
> 
> ### ** Examples
> 
> 
> iris %>%
+ auto_variable_contributions(
+  tidy_formula(., target = Petal.Width)
+  )
Error in setinfo.xgb.DMatrix(dmat, names(p), p[[1]]) : 
  The length of labels must equal to the number of rows in the input data
Calls: %>% -> auto_variable_contributions
Timing stopped at: 0.008 0 0.027
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘autostats.Rmd’ using rmarkdown
Quitting from lines 41-43 (autostats.Rmd) 
Error: processing vignette 'autostats.Rmd' failed with diagnostics:
The length of labels must equal to the number of rows in the input data
--- failed re-building ‘autostats.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinycssloaders’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘readxl’ ‘reshape2’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘bslib’ ‘rclipboard’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘jose’ ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘httr’ ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
CRexp_set: no visible global function definition for ‘runif’
b6e6rl: no visible global function definition for ‘runif’
derand_RL: no visible global function definition for ‘runif’
derandexp_RL: no visible global function definition for ‘runif’
nahvyb_expt: no visible global function definition for ‘runif’
roulete: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
.generateTransform: no visible global function definition for ‘sd’
.generateUnitHyperCube: no visible global function definition for
  ‘runif’
.makeBoundedSingleStep: no visible global function definition for
  ‘runif’
.makeBoundedStep: no visible global function definition for ‘runif’
.makeStep: no visible global function definition for ‘runif’
.staircaseSampling: no visible global function definition for ‘runif’
GaussianPrior: no visible global function definition for ‘qnorm’
LogNormalPrior: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm runif sd
Consider adding
  importFrom("stats", "qnorm", "runif", "sd")
to your NAMESPACE file.
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.
Note: found 64209 marked UTF-8 strings
Namespace in Imports field not imported from: ‘glpkAPI’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
BACprior.CV: no visible global function definition for ‘na.fail’
BACprior.CV: no visible global function definition for ‘abline’
BACprior.boot: no visible global function definition for ‘na.fail’
BACprior.boot: no visible global function definition for ‘abline’
BACprior.lm: no visible global function definition for ‘na.fail’
BACprior.lm: no visible global function definition for ‘coef’
BACprior.lm: no visible global function definition for ‘vcov’
Undefined global functions or variables:
  abline coef na.fail vcov
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "coef", "na.fail", "vcov")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘mvtnorm’ which was already attached by Depends.
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘tkrplot’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Running ‘spelling.R’
  Running ‘testthat.R’ [90s/109s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(baguette)
  Loading required package: parsnip
  > 
  > test_check("baguette")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-C5.R:99:3): check C5 parsnip interface ────────────────────────
  nrow(class_mod_pred) not equal to 5.
  1/1 mismatches
  [1] 1 - 5 == -4
  ── Failure (test-C5.R:129:3): check C5 parsnip interface ───────────────────────
  nrow(class_cost_pred) not equal to 5.
  1/1 mismatches
  [1] 1 - 5 == -4
  ── Failure (test-cart.R:148:3): check CART parsnip interface ───────────────────
  names(reg_mod_pred) not equal to ".pred".
  1/1 mismatches
  x[1]: ".pred_"
  y[1]: ".pred"
  ── Failure (test-cart.R:169:3): check CART parsnip interface ───────────────────
  nrow(class_cost_pred) not equal to 5.
  1/1 mismatches
  [1] 1 - 5 == -4
  ── Failure (test-cart.R:201:3): check CART parsnip interface ───────────────────
  nrow(class_mod_pred) not equal to 5.
  1/1 mismatches
  [1] 1 - 5 == -4
  ── Failure (test-mars.R:122:3): check MARS parsnip interface ───────────────────
  names(reg_mod_pred) not equal to ".pred".
  1/1 mismatches
  x[1]: ".pred_"
  y[1]: ".pred"
  ── Failure (test-mars.R:145:3): check MARS parsnip interface ───────────────────
  nrow(reg_class_pred) not equal to 5.
  1/1 mismatches
  [1] 1 - 5 == -4
  
  [ FAIL 7 | WARN 26 | SKIP 0 | PASS 149 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Found the following files/directories:
  ‘exemplary_input1.txt’ ‘exemplary_input2.txt’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats4’
  All declared Imports should be used.
Running examples in ‘bamlss-Ex.R’ failed
The error most likely occurred in:

> ### Name: GAMart
> ### Title: GAM Artificial Data Set
> ### Aliases: GAMart
> ### Keywords: datasets
> 
> ### ** Examples
> 
> d <- GAMart()
Error in `[.data.frame`(x, nodups) : undefined columns selected
Calls: GAMart -> match.index -> [ -> [.data.frame
Execution halted
Running examples in ‘BaM-Ex.R’ failed
The error most likely occurred in:

> ### Name: iq
> ### Title: iq data frame
> ### Aliases: iq
> 
> ### ** Examples
> 
> ## Not run: 
> {
+ data(iq)
+ n <- length(iq[1,])
+ t.iq <- (iq[1,]-mean(as.numeric(iq)))/(sd(iq[1,])/sqrt(n))
+ r.t <- (rt(100000, n-1)*(sd(iq)/sqrt(n))) + mean(as.numeric(iq))
+ quantile(r.t,c(0.01,0.10,0.25,0.5,0.75,0.90,0.99))
+ r.sigma.sq <- 1/rgamma(100000,shape=(n-2)/2, rate=var(as.numeric(iq))*(n-1)/2)
+ quantile(sqrt(r.sigma.sq), c(0.01,0.10,0.25,0.5,0.75,0.90,0.99))
+ }
Warning in rt(1e+05, n - 1) * (sd(iq)/sqrt(n)) :
  longer object length is not a multiple of shorter object length
Error: dims [product 6561] do not match the length of object [100000]
Execution halted
best_binomial_bandit : f: no visible global function definition for
  ‘dbeta’
best_binomial_bandit : f: no visible global function definition for
  ‘pbeta’
best_binomial_bandit: no visible global function definition for
  ‘integrate’
best_poisson_bandit : f: no visible global function definition for
  ‘dgamma’
best_poisson_bandit : f: no visible global function definition for
  ‘pgamma’
best_poisson_bandit: no visible global function definition for
  ‘integrate’
deseasonalized_trend: no visible global function definition for
  ‘predict’
distribution_estimate: no visible global function definition for
  ‘quantile’
distribution_estimate: no visible global function definition for
  ‘qbeta’
significance_analysis: no visible global function definition for
  ‘prop.test’
sim_post: no visible global function definition for ‘rbeta’
summarize_metrics: no visible global function definition for ‘median’
summarize_metrics: no visible global function definition for
  ‘prop.test’
Undefined global functions or variables:
  dbeta dgamma integrate median pbeta pgamma predict prop.test qbeta
  quantile rbeta
Consider adding
  importFrom("stats", "dbeta", "dgamma", "integrate", "median", "pbeta",
             "pgamma", "predict", "prop.test", "qbeta", "quantile",
             "rbeta")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Note: found 148 marked UTF-8 strings
extractAffybatch: no visible global function definition for ‘new’
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'LazyData' is specified without a 'data' directory
'library' or 'require' calls to packages already attached by Depends:
  ‘grid’ ‘lattice’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘grid’ ‘lattice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
barcode: no visible global function definition for ‘unit’
barcode: no visible global function definition for ‘grid.newpage’
barcode: no visible global function definition for ‘grid.text’
barcode: no visible global function definition for ‘gpar’
barcode: no visible global function definition for ‘pushViewport’
barcode: no visible global function definition for ‘viewport’
barcode: no visible global function definition for ‘convertHeight’
barcode: no visible global function definition for ‘convertWidth’
barcode: no visible global function definition for ‘grid.rect’
barcode: no visible global function definition for ‘popViewport’
barcode.panel: no visible global function definition for ‘unit’
barcode.panel: no visible global function definition for ‘hist’
barcode.panel: no visible global function definition for ‘pushViewport’
barcode.panel: no visible global function definition for ‘viewport’
barcode.panel: no visible global function definition for ‘grid.xaxis’
barcode.panel: no visible global function definition for ‘gpar’
barcode.panel: no visible global function definition for ‘grid.text’
barcode.panel: no visible global function definition for ‘popViewport’
barcode.panel: no visible global function definition for
  ‘grid.segments’
barcode.panel: no visible global function definition for ‘grid.points’
Undefined global functions or variables:
  convertHeight convertWidth gpar grid.newpage grid.points grid.rect
  grid.segments grid.text grid.xaxis hist popViewport pushViewport unit
  viewport
Consider adding
  importFrom("graphics", "hist")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Note: found 13825 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvnfast’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘the-BART-R-package.Rnw’ using knitr
Warning in remind_sweave(if (in.file) input, sweave_lines) :
  It seems you are using the Sweave-specific syntax in line(s) 10; you may need Sweave2knitr("the-BART-R-package.Rnw") to convert it to knitr
Error: processing vignette 'the-BART-R-package.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'the-BART-R-package.tex' failed.
LaTeX errors:
! Package xcolor Error: Undefined color `Blue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `Blue'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `Red'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
--- failed re-building ‘the-BART-R-package.Rnw’

SUMMARY: processing the following file failed:
  ‘the-BART-R-package.Rnw’

Error: Vignette re-building failed.
Execution halted
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.
Namespaces in Imports field not imported from:
  ‘dbplyr’ ‘dotenv’ ‘googleAuthR’ ‘httr’ ‘writexl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘splines’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
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 ‘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.
Namespaces in Imports field not imported from:
  ‘circlize’ ‘hexbin’ ‘scales’ ‘sna’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘rPython’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 19 marked UTF-8 strings
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.
Namespaces in Imports field not imported from:
  ‘scales’ ‘utils’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
FECRT: no visible global function definition for ‘pdf’
FECRT: no visible global function definition for ‘hist’
FECRT: no visible global function definition for ‘abline’
FECRT: no visible global function definition for ‘dev.off’
FECRT.analysis: no visible global function definition for ‘pdf’
FECRT.analysis: no visible global function definition for ‘hist’
FECRT.analysis: no visible global function definition for ‘abline’
FECRT.analysis: no visible global function definition for ‘dev.off’
fecrt: no visible global function definition for ‘pdf’
fecrt: no visible global function definition for ‘hist’
fecrt: no visible global function definition for ‘abline’
fecrt: no visible global function definition for ‘dev.off’
fecrt.analysis: no visible global function definition for ‘pdf’
fecrt.analysis: no visible global function definition for ‘hist’
fecrt.analysis: no visible global function definition for ‘abline’
fecrt.analysis: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  abline dev.off hist pdf
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "hist")
to your NAMESPACE file.
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:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MatrixModels’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘StanHeaders’ ‘astsa’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘RcppParallel’ ‘mlbench’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
File ‘BayesGPfit/libs/BayesGPfit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
BMAnimalTrack: no visible global function definition for ‘nlm’
BMAnimalTrack: no visible global function definition for ‘qnorm’
dataSim: no visible global function definition for ‘rnorm’
rBBridge: no visible global function definition for ‘rnorm’
rBMotion: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  nlm qnorm rnorm
Consider adding
  importFrom("stats", "nlm", "qnorm", "rnorm")
to your NAMESPACE file.
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.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘shinytest’ ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘FastGP’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘workflows’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cyjShiny’
Malformed Description field: should contain one or more complete sentences.
noninform_prior : a : f1: no visible global function definition for
  ‘pbeta’
noninform_prior : a : f1: no visible global function definition for
  ‘dbeta’
noninform_prior : a: no visible global function definition for
  ‘integrate’
noninform_prior: no visible global function definition for ‘rbeta’
noninform_prior: no visible global function definition for ‘optim’
postNullFun : b : f1: no visible global function definition for ‘pbeta’
postNullFun : b : f1: no visible global function definition for ‘dbeta’
postNullFun : b: no visible global function definition for ‘integrate’
prior_prob : a : f1: no visible global function definition for ‘pbeta’
prior_prob : a : f1: no visible global function definition for ‘dbeta’
prior_prob : a: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  dbeta integrate optim pbeta rbeta
Consider adding
  importFrom("stats", "dbeta", "integrate", "optim", "pbeta", "rbeta")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘fda’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘HDInterval’ ‘MCMCpack’ ‘R2WinBUGS’ ‘R2jags’ ‘carData’ ‘rjags’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RcppNumerical’
  All declared Imports should be used.
MHratioPopPref: no visible global function definition for ‘runif’
MratioPopMult: no visible global function definition for ‘dunif’
MratioPopMult: no visible global function definition for ‘runif’
bayesPref: no visible global function definition for ‘runif’
calcP: no visible global function definition for ‘dunif’
calcP: no visible global function definition for ‘dmultinom’
calcdic: no visible global function definition for ‘median’
calcdic: no visible binding for global variable ‘median’
calcdic: no visible global function definition for ‘dmultinom’
calcdicExtern: no visible global function definition for ‘median’
calcdicExtern: no visible global function definition for ‘dmultinom’
calcdicExtern: no visible binding for global variable ‘median’
credibleIntervals: no visible global function definition for ‘quantile’
prefPlot: no visible global function definition for ‘postscript’
prefPlot: no visible global function definition for ‘lines’
prefPlot: no visible global function definition for ‘density’
prefPlot: no visible global function definition for ‘median’
prefPlot: no visible global function definition for ‘legend’
prefPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  density dev.off dmultinom dunif legend lines median postscript
  quantile runif
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "density", "dmultinom", "dunif", "median",
             "quantile", "runif")
to your NAMESPACE file.
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.
Note: found 1924 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘matrixcalc’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘MASS’ ‘combinat’ ‘gplots’ ‘mnormt’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
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.
validate: no visible binding for global variable ‘qnorm’
validate: no visible global function definition for ‘pchisq’
validate: no visible global function definition for ‘qnorm’
validate: no visible global function definition for ‘axis’
validate: no visible global function definition for ‘points’
validate: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis pchisq points qnorm
Consider adding
  importFrom("graphics", "abline", "axis", "points")
  importFrom("stats", "pchisq", "qnorm")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'library' or 'require' call to ‘coda’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Rd file 'BPSpostSample.Rd':
  \usage lines wider than 90 characters:
     BPSpostSample(hyp, times, obs = NULL, mclen = 10, burnin = 0, thin = 1, df = 10, etastar = NULL)
  \examples lines wider than 100 characters:
     post<-BPSpostSample(hypars, times = earthquakes$ti, obs = earthquakes$ob, etastar = postmode$etastar)

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘diagnostics.pdf’ ‘post.rda’
Packages in Depends field not imported from:
  ‘fields’ ‘poibin’ ‘rjags’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
BMR.plot: no visible global function definition for ‘heat.colors’
BMR.plot: no visible global function definition for ‘image.plot’
BMR.plot: no visible global function definition for ‘title’
BMR.plot: no visible global function definition for ‘mtext’
BMR.plot: no visible global function definition for ‘par’
baysic.data: no visible global function definition for ‘layout’
baysic.data: no visible global function definition for ‘barplot’
baysic.data: no visible global function definition for ‘rainbow’
baysic.fit: no visible global function definition for ‘jags.model’
baysic.fit: no visible global function definition for ‘update’
baysic.fit: no visible global function definition for ‘coda.samples’
baysic.test: no visible global function definition for ‘ppois’
baysic.test : <anonymous>: no visible global function definition for
  ‘ppoibin’
baysic.test: no visible global function definition for ‘pbinom’
fuzzy.FDR.approx: no visible global function definition for ‘p.adjust’
fuzzy.FDR.approx: no visible global function definition for ‘runif’
Undefined global functions or variables:
  barplot coda.samples heat.colors image.plot jags.model layout mtext
  p.adjust par pbinom ppoibin ppois rainbow runif title update
Consider adding
  importFrom("grDevices", "heat.colors", "rainbow")
  importFrom("graphics", "barplot", "layout", "mtext", "par", "title")
  importFrom("stats", "p.adjust", "pbinom", "ppois", "runif", "update")
to your NAMESPACE file.
Rd file 'baysic.fit.Rd':
  \usage lines wider than 90 characters:
     baysic.fit(dat.out, snv.cat, covar = NULL, excl.list = NULL, burn.in = 10000,n.samp = 25000, fn.jags = "baysic.jags", prior = NULL)
  \examples lines wider than 100 characters:
     snv.cat.ex[[2]]<-unique(c(grep("TC.",colnames(ccds.19)[-c(1:2)]),grep(".CG",colnames(ccds.19)[-c(1:2)])))

Rd file 'baysic.test.Rd':
  \usage lines wider than 90 characters:
     baysic.test(dat.out, fit.out, fdr.level = 0.15, fuzzy.cnt = 10000, r = NULL,subtype = NULL, PB.approx = FALSE)
  \examples lines wider than 100 characters:
     snv.cat.ex[[2]]<-unique(c(grep("TC.",colnames(ccds.19)[-c(1:2)]),grep(".CG",colnames(ccds.19)[-c(1:2)])))

These lines will be truncated in the PDF manual.
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘matrixStats’ ‘reshape2’ ‘scales’
  All declared Imports should be used.
BAYSTAR: no visible global function definition for ‘median’
BAYSTAR: no visible global function definition for ‘ar’
BAYSTAR: no visible global function definition for ‘quantile’
BAYSTAR: no visible global function definition for ‘dev.new’
BAYSTAR: no visible global function definition for ‘ts.plot’
BAYSTAR: no visible global function definition for ‘title’
BAYSTAR: no visible global function definition for ‘par’
BAYSTAR: no visible global function definition for ‘plot.ts’
BAYSTAR: no visible global function definition for ‘lines’
BAYSTAR: no visible global function definition for ‘acf’
TAR.lagd: no visible global function definition for ‘runif’
TAR.sigma: no visible global function definition for ‘rgamma’
TAR.simu: no visible global function definition for ‘rnorm’
TAR.summary: no visible global function definition for ‘quantile’
TAR.summary: no visible global function definition for ‘sd’
TAR.thres: no visible global function definition for ‘rnorm’
TAR.thres: no visible global function definition for ‘runif’
Undefined global functions or variables:
  acf ar dev.new lines median par plot.ts quantile rgamma rnorm runif
  sd title ts.plot
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "lines", "par", "title")
  importFrom("stats", "acf", "ar", "median", "plot.ts", "quantile",
             "rgamma", "rnorm", "runif", "sd", "ts.plot")
to your NAMESPACE file.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(baytrends)
  Loading:baytrends v2.0.5
  
  Attaching package: 'baytrends'
  
  The following object is masked from 'package:stats':
  
      nobs
  
  > 
  > test_check("baytrends")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-impute.R:42:3): impute, norm ────────────────────────────────────
  Error in `mledist(censdata, distname, start = arg_startfix$start.arg, fix.arg = arg_startfix$fix.arg, 
      checkstartfix = TRUE, ...)`: data must be a numeric vector of length greater than 1 for non censored data or a dataframe with two columns named left and right and more than one line for censored data
  Backtrace:
      █
   1. └─baytrends::impute(x, "norm") test-impute.R:42:2
   2.   └─fitdistrplus::fitdistcens(myData1, distr = "norm")
   3.     └─fitdistrplus::mledist(...)
  ── Error (test-impute.R:55:3): impute, lnorm ───────────────────────────────────
  Error in `mledist(censdata, distname, start = arg_startfix$start.arg, fix.arg = arg_startfix$fix.arg, 
      checkstartfix = TRUE, ...)`: data must be a numeric vector of length greater than 1 for non censored data or a dataframe with two columns named left and right and more than one line for censored data
  Backtrace:
      █
   1. └─baytrends::impute(x, "lnorm") test-impute.R:55:2
   2.   └─fitdistrplus::fitdistcens(myData1, distr = "lnorm")
   3.     └─fitdistrplus::mledist(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 12 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package in Depends field not imported from: ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Malformed Description field: should contain one or more complete sentences.
LaplaceMetropolis_admkr: no visible binding for global variable
  ‘median’
LaplaceMetropolis_admkr: no visible global function definition for
  ‘mad’
LaplaceMetropolis_gaussian: no visible binding for global variable
  ‘median’
LaplaceMetropolis_gaussian: no visible global function definition for
  ‘mad’
cost_admkr: no visible global function definition for ‘sd’
cov_chol: no visible global function definition for ‘qchisq’
cov_chol_admkr: no visible global function definition for ‘qchisq’
gibbs_admkr_erro: no visible global function definition for ‘rnorm’
gibbs_admkr_erro: no visible global function definition for ‘runif’
gibbs_admkr_nw: no visible global function definition for ‘qnorm’
gibbs_admkr_nw: no visible global function definition for ‘rnorm’
gibbs_admkr_nw: no visible global function definition for ‘runif’
loglikelihood_admkr: no visible global function definition for ‘sd’
margin_like_admkr: no visible global function definition for ‘sd’
np_gibbs: no visible global function definition for ‘qnorm’
np_gibbs: no visible global function definition for ‘rnorm’
np_gibbs: no visible global function definition for ‘runif’
np_gibbs: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  mad median qchisq qnorm rgamma rnorm runif sd
Consider adding
  importFrom("stats", "mad", "median", "qchisq", "qnorm", "rgamma",
             "rnorm", "runif", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
bbmm.contour: no visible global function definition for ‘na.omit’
bbmm.contour: no visible global function definition for ‘optimize’
bbmm.contour: no visible global function definition for ‘contour’
bbmm.contour: no visible global function definition for ‘points’
bbmm.contour: no visible global function definition for ‘lines’
brownian.bridge: no visible global function definition for ‘sd’
brownian.motion.variance: no visible global function definition for
  ‘optimize’
Undefined global functions or variables:
  contour lines na.omit optimize points sd
Consider adding
  importFrom("graphics", "contour", "lines", "points")
  importFrom("stats", "na.omit", "optimize", "sd")
to your NAMESPACE file.
bbo: no visible global function definition for ‘runif’
bbo: no visible global function definition for ‘tail’
Undefined global functions or variables:
  runif tail
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘locfit’ ‘secr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘latticeExtra’ ‘rgdal’
  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.
Found the following files/directories:
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_50_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_50_biascor_1.RData’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘fabiabreast.txt’
pairs.bce : panel.cor: no visible global function definition for ‘text’
pairs.bce : panel.cor: no visible global function definition for ‘cor’
pairs.bce : panel.hist: no visible global function definition for ‘par’
pairs.bce : panel.hist: no visible global function definition for
  ‘hist’
pairs.bce : panel.hist: no visible global function definition for
  ‘rect’
pairs.bce: no visible global function definition for ‘pairs’
panel.cor: no visible global function definition for ‘par’
panel.cor: no visible global function definition for ‘cor’
panel.cor: no visible global function definition for ‘strwidth’
panel.cor: no visible global function definition for ‘text’
rdirichlet2: no visible global function definition for ‘rgamma’
summary.bce: no visible global function definition for ‘cov’
summary.bce: no visible binding for global variable ‘sd’
summary.bce: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  cor cov hist pairs par quantile rect rgamma sd strwidth text
Consider adding
  importFrom("graphics", "hist", "pairs", "par", "rect", "strwidth",
             "text")
  importFrom("stats", "cor", "cov", "quantile", "rgamma", "sd")
to your NAMESPACE file.
Running examples in ‘BCE-Ex.R’ failed
The error most likely occurred in:

> ### Name: BCE
> ### Title: Bayesian Composition Estimator
> ### Aliases: BCE
> ### Keywords: models
> 
> ### ** Examples
> 
> ##====================================
> 
> # example using bceInput data
> # first try
> 
> X <- BCE(bceInput$Rat,bceInput$Dat,relsdRat=.2,relsdDat=.2,
+          iter=1000,outputlength=5000,jmpX=.01,jmpRat=.01)
Error in lsei(A, B, E, F, G, H) : 
  cannot solve least squares problem - A and B not compatible
Calls: BCE ... with.default -> eval -> eval -> lsei2 -> lsei1 -> lsei
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘coda’ ‘knitr’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
bcpmeta.model: no visible global function definition for ‘rbinom’
bcpmeta.model: no visible global function definition for ‘runif’
bcpmeta.parameters: no visible global function definition for ‘runif’
cp.plot: no visible global function definition for ‘postscript’
cp.plot: no visible global function definition for ‘lines’
cp.plot: no visible global function definition for ‘axis’
cp.plot: no visible global function definition for ‘box’
cp.plot: no visible global function definition for ‘points’
cp.plot: no visible global function definition for ‘dev.off’
lMarLik.EB.normAR: no visible global function definition for ‘optimize’
lMarLik.normAR: no visible global function definition for ‘integrate’
marginal.plot: no visible global function definition for ‘postscript’
marginal.plot: no visible global function definition for ‘axis’
marginal.plot: no visible global function definition for ‘box’
marginal.plot: no visible global function definition for ‘points’
marginal.plot: no visible global function definition for ‘dev.off’
simgen: no visible global function definition for ‘rnorm’
up.eta.MH.normAR: no visible global function definition for ‘runif’
up.eta.RS.normAR: no visible global function definition for ‘runif’
up.parameters.EB.normAR: no visible global function definition for
  ‘rnorm’
up.parameters.normAR: no visible global function definition for ‘rnorm’
up.parameters.normAR: no visible global function definition for ‘runif’
up.parameters.normAR: no visible global function definition for
  ‘rgamma’
Undefined global functions or variables:
  axis box dev.off integrate lines optimize points postscript rbinom
  rgamma rnorm runif
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "axis", "box", "lines", "points")
  importFrom("stats", "integrate", "optimize", "rbinom", "rgamma",
             "rnorm", "runif")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rlang’
  All declared Imports should be used.
Package suggested but not available for checking: ‘webshot2’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'kBET', 'lisi', 'dlfUtils'
Namespace in Imports field not imported from: ‘splatter’
  All declared Imports should be used.
Note: found 72 marked UTF-8 strings
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
mise: no visible global function definition for ‘integrate’
density,BrVitale : density.vitale : <anonymous>: no visible global
  function definition for ‘dbeta’
density,Chen99Kernel : <anonymous>: no visible global function
  definition for ‘dbeta’
density,HirukawaJLNKernel : <anonymous>: no visible global function
  definition for ‘dbeta’
density,MicroBetaChen99Kernel : <anonymous>: no visible global function
  definition for ‘dbeta’
density,Vitale : <anonymous>: no visible global function definition for
  ‘dbeta’
distribution,BernsteinPolynomials : <anonymous>: no visible global
  function definition for ‘integrate’
distribution,KernelDensity : <anonymous>: no visible global function
  definition for ‘integrate’
print,BoundedDensity: no visible global function definition for ‘str’
print,KernelDensity: no visible global function definition for ‘str’
rsample,BoundedDensity: no visible global function definition for
  ‘runif’
setNormalizationConst,MacroBetaChen99Kernel: no visible global function
  definition for ‘integrate’
setNormalizationConst,MacroBetaHirukawaTSKernel: no visible global
  function definition for ‘integrate’
setNormalizationConstant,MacroBetaHirukawaJLNKernel: no visible global
  function definition for ‘integrate’
setNormalizationConstants,MicroBetaChen99Kernel :
  density.kernelFunction: no visible global function definition for
  ‘dbeta’
setNormalizationConstants,MicroBetaChen99Kernel : <anonymous>: no
  visible global function definition for ‘integrate’
show,BoundedDensity: no visible global function definition for ‘str’
show,KernelDensity: no visible global function definition for ‘str’
Undefined global functions or variables:
  dbeta integrate runif str
Consider adding
  importFrom("stats", "dbeta", "integrate", "runif")
  importFrom("utils", "str")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘dump.txt’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘bferrbars.eps’ ‘dataplot.eps’ ‘ppdat.eps’ ‘ppmod.eps’
Packages in Depends field not imported from:
  ‘RColorBrewer’ ‘beadarray’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
beadtypeFilter: no visible global function definition for ‘na.omit’
beadtypeFilter: no visible global function definition for ‘exprs’
beadtypeFilter: no visible global function definition for ‘se.exprs’
beadtypeFilter: no visible global function definition for ‘beadNum’
beadtypeFilter: no visible global function definition for ‘fData’
emCDF: no visible global function definition for ‘brewer.pal’
emCDF: no visible global function definition for ‘ecdf’
emCDF: no visible global function definition for ‘legend’
emCDF: no visible global function definition for ‘lines’
emCDF: no visible global function definition for ‘text’
emCDF: no visible global function definition for ‘reshape’
iccFun : <anonymous>: no visible global function definition for
  ‘quantile’
varianceplot: no visible global function definition for ‘reshape’
varianceplot: no visible global function definition for ‘points’
varianceplot: no visible global function definition for ‘legend’
Undefined global functions or variables:
  beadNum brewer.pal ecdf exprs fData legend lines na.omit points
  quantile reshape se.exprs text
Consider adding
  importFrom("graphics", "legend", "lines", "points", "text")
  importFrom("stats", "ecdf", "na.omit", "quantile", "reshape")
to your NAMESPACE file.
Rd file 'iccFun.Rd':
  \examples lines wider than 100 characters:
     aaa<-na.omit(data.frame(I(rownames(exprs(exampleSummaryDataNorm))),exprs(exampleSummaryDataNorm)))[1:40,]

These lines will be truncated in the PDF manual.
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
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.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘beast_plot_toy.pdf’
Found the following files/directories:
  ‘example_Initial.parameters.Robj’ ‘example_MCMC_output1.Robj’
Namespaces in Imports field not imported from:
  ‘htmltools’ ‘rstudioapi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘alist.txt’ ‘rpkg’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
Namespace in Imports field not imported from: ‘BiDAG’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘compiler’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘ggplot2’ ‘readxl’ ‘rlist’ ‘shinyBS’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘coda’ ‘splines’
  All declared Imports should be used.
Note: found 20 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Non-standard file/directory found at top level:
  ‘extdata’
betafam: no visible global function definition for ‘pnorm’
betafam: no visible global function definition for ‘pchisq’
betafam: no visible global function definition for ‘lm’
betafam: no visible global function definition for ‘coefficients’
betafam: no visible global function definition for ‘glm.fit’
betafam: no visible global function definition for ‘gaussian’
betafam: no visible global function definition for ‘glmnet’
Undefined global functions or variables:
  coefficients gaussian glm.fit glmnet lm pchisq pnorm
Consider adding
  importFrom("stats", "coefficients", "gaussian", "glm.fit", "lm",
             "pchisq", "pnorm")
to your NAMESPACE file.
Rd file 'betafam.Rd':
  \usage lines wider than 90 characters:
     betafam(ped,group.threshold=-1,fix.group.index=NULL, fix.weight=NULL,mute.SMM=TRUE,trait=c("binary","qtl"),LC.test=c("LC.true","LC","si ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Checking should be performed on sources prepared by ‘R CMD build’.
'LazyData' is specified without a 'data' directory
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.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Note: found 10089 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
block.gibbs: no visible global function definition for ‘rmultinom’
rdirichlet: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  rgamma rmultinom
Consider adding
  importFrom("stats", "rgamma", "rmultinom")
to your NAMESPACE file.
Note: found 772 marked UTF-8 strings
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
global: no visible global function definition for ‘par’
global: no visible global function definition for ‘runif’
global: no visible global function definition for ‘cov’
mymcmc: no visible global function definition for ‘par’
mymcmc: no visible global function definition for ‘rnorm’
mymcmc: no visible global function definition for ‘runif’
mymcmc: no visible global function definition for ‘cov’
mymcmc: no visible global function definition for ‘lines’
plkhci: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  cov lines par qchisq rnorm runif
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "cov", "qchisq", "rnorm", "runif")
to your NAMESPACE file.
Package in Depends field not imported from: ‘betareg’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bias: no visible global function definition for ‘predict’
bias: no visible global function definition for ‘pnorm’
bias: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  model.matrix pnorm predict
Consider adding
  importFrom("stats", "model.matrix", "pnorm", "predict")
to your NAMESPACE file.
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.
'LazyData' is specified without a 'data' directory
Note: found 99 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘DAAG’ ‘datasets’ ‘expm’ ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nycflights13’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RBGL’
  All declared Imports should be used.
Found the following files/directories:
  ‘BiDimRegrOutput.txt’
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘svyPVpack’
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
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.
GNU make is a SystemRequirements.
Running examples in ‘bigmatch-Ex.R’ failed
The error most likely occurred in:

> ### Name: check
> ### Title: Check SMDs of the matched data set.
> ### Aliases: check
> 
> ### ** Examples
> 
> # To run this example, you must load the optmatch package.
> 
> # Caliper of .2 on the propensity score, near fine balance of
> # education, a robust Mahalanobis distrance for X.
> data(nh0506)
> attach(nh0506)
> X<-cbind(female,age,black,hispanic,education,povertyr,bmi)
> m<-nfmatch(z=z,p=propens,fine=education,X=X,caliper=.2,dat=nh0506,rank=FALSE)
> matcheddata<-m$data
> Xm<-subset(matcheddata, select=c('female','age','black','hispanic','education','povertyr','bmi'))
> check(X,Xm,z,matcheddata$z)
Error in mdata[which(mz == 0), ] : subscript out of bounds
Calls: check
Execution halted
possible bashism in configure line 14 (echo -n):
  echo -n "  checking for Sun Studio compiler..."
  possible bashism in configure line 24 (echo -n):
  echo -n "  checking for OS..."
Checking should be performed on sources prepared by ‘R CMD build’.
'LazyData' is specified without a 'data' directory
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.
Found the following files/directories:
  ‘outputs’
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
possible bashism in configure line 13 (echo -n):
  echo -n "  checking for Sun Studio compiler..."
  possible bashism in configure line 23 (echo -n):
  echo -n "  checking for OS..."
File ‘bigtabulate/libs/bigtabulate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘gbm’ ‘glmnet’ ‘randomForest’ ‘tree’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LDCAEst: no visible global function definition for ‘glmnet’
cv.LDCA: no visible global function definition for ‘cv.glmnet’
predict.LDCA: no visible global function definition for ‘predict’
predict.cv.LDCA: no visible global function definition for ‘predict’
predict.tsp.gbm: no visible global function definition for ‘predict’
predict.tsp.randomForest: no visible global function definition for
  ‘predict’
predict.tsp.tree: no visible global function definition for ‘predict’
tsp.gbm: no visible global function definition for ‘gbm.fit’
tsp.randomForest: no visible global function definition for
  ‘randomForest’
tsp.tree: no visible global function definition for ‘tree.control’
tsp.tree: no visible global function definition for ‘tree’
Undefined global functions or variables:
  cv.glmnet gbm.fit glmnet predict randomForest tree tree.control
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Rd file 'predict.LDCA.Rd':
  \usage lines wider than 90 characters:
     predict(object, newx, s = NULL, type = c("link", "response", "coefficients", "nonzero", "class"), exact = FALSE, offset, ...)

Rd file 'predict.tsp.randomForest.Rd':
  \usage lines wider than 90 characters:
     predict(object, newdata, type = "response", norm.votes = TRUE, predict.all = FALSE, proximity = FALSE, nodes = FALSE, cutoff, ...)

Rd file 'predict.tsp.tree.Rd':
  \usage lines wider than 90 characters:
     predict(object, newdata, type = c("vector", "tree", "class", "where"), split = FALSE, nwts, eps = 0.001, ...)

Rd file 'tsp.gbm.Rd':
  \usage lines wider than 90 characters:
     tsp.gbm(x, y, offset = NULL, misc = NULL, distribution = "bernoulli", w = NULL, var.monotone = NULL, n.trees = 100, interaction.depth = ... [TRUNCATED]

Rd file 'tsp.randomForest.Rd':
  \usage lines wider than 90 characters:
     tsp.randomForest(x, y = NULL, xtest = NULL, ytest = NULL, ntree = 500, type = "classification", mtry = if (!is.null(y) && !is.factor(y) ... [TRUNCATED]

Rd file 'tsp.tree.Rd':
  \usage lines wider than 90 characters:
     tsp.tree(X, response, control = tree.control(dim(X)[1], ...), method = "recursive.partition", split = c("deviance", "gini"), x = FALSE, ... [TRUNCATED]

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

> ### Name: bb_densityplot
> ### Title: Helper for creating a density plot
> ### Aliases: bb_densityplot
> 
> ### ** Examples
> 
> 
> # With a vector
> billboarder() %>%
+   bb_densityplot(data = rnorm(1e4))
> 
> data("diamonds", package = "ggplot2")
> 
> # density plot with one variable
> billboarder() %>% 
+   bb_densityplot(data = diamonds, x = "carat")
Error in density.default(x = data[[x]], bw = bw, adjust = adjust, kernel = kernel,  : 
  argument 'x' must be numeric
Calls: %>% -> bb_densityplot -> <Anonymous> -> density.default
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(billboarder)
  > 
  > test_check("billboarder")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-bb_helpers.R:175:3): bb_linechart works ─────────────────────────
  Error in `FUN(X[[i]], ...)`: object 'Sine' not found
  Backtrace:
      █
   1. ├─`%>%`(...) test-bb_helpers.R:175:2
   2. └─billboarder::bb_linechart(...)
   3.   └─billboarder:::bbmapping(data = data, mapping = mapping)
   4.     └─base::lapply(X = mapping, FUN = eval_tidy, data = data)
   5.       └─rlang:::FUN(X[[i]], ...)
  ── Error (test-readme.R:293:3): Histogram & density - grouped ──────────────────
  Error: Aesthetics must be valid data columns. Problematic aesthetic(s): x = sample. 
  Did you mistype the name of a data column or forget to add after_stat()?
  Backtrace:
       █
    1. ├─`%>%`(...) test-readme.R:293:2
    2. ├─billboarder::bb_x_grid(...)
    3. │ └─billboarder:::.bb_opt(bb, "grid", x = list(...))
    4. └─billboarder::bb_histogram(...)
    5.   └─ggplot2::layer_data(p, i = 1L)
    6.     ├─ggplot2::ggplot_build(plot)
    7.     └─ggplot2:::ggplot_build.ggplot(plot)
    8.       └─ggplot2:::by_layer(function(l, d) l$compute_aesthetics(d, plot))
    9.         └─ggplot2:::f(l = layers[[i]], d = data[[i]])
   10.           └─l$compute_aesthetics(d, plot)
   11.             └─ggplot2:::f(..., self = self)
  
  [ FAIL 2 | WARN 5 | SKIP 0 | PASS 210 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘billboarder-intro.Rmd’ using rmarkdown
--- finished re-building ‘billboarder-intro.Rmd’

--- re-building ‘billboarder-mapping.Rmd’ using rmarkdown
Quitting from lines 53-55 (billboarder-mapping.Rmd) 
Error: processing vignette 'billboarder-mapping.Rmd' failed with diagnostics:
arguments imply differing number of rows: 2, 5
--- failed re-building ‘billboarder-mapping.Rmd’

--- re-building ‘billboarder-options.Rmd’ using rmarkdown
--- finished re-building ‘billboarder-options.Rmd’

--- re-building ‘billboarder.Rmd’ using rmarkdown
Quitting from lines 271-312 (billboarder.Rmd) 
Error: processing vignette 'billboarder.Rmd' failed with diagnostics:
arguments imply differing number of rows: 11, 48
--- failed re-building ‘billboarder.Rmd’

--- re-building ‘lines-options.Rmd’ using rmarkdown
Quitting from lines 75-81 (lines-options.Rmd) 
Error: processing vignette 'lines-options.Rmd' failed with diagnostics:
cannot coerce type 'closure' to vector of type 'character'
--- failed re-building ‘lines-options.Rmd’

--- re-building ‘linked-tooltip.Rmd’ using rmarkdown
--- finished re-building ‘linked-tooltip.Rmd’

SUMMARY: processing the following files failed:
  ‘billboarder-mapping.Rmd’ ‘billboarder.Rmd’ ‘lines-options.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 660 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
chisq.sim.factory : chisq.sim.func: no visible global function
  definition for ‘chisq.test’
rmultnom: no visible global function definition for ‘runif’
Undefined global functions or variables:
  chisq.test runif
Consider adding
  importFrom("stats", "chisq.test", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘ccf_ccf_ID31_ID32_res.jpg’ ‘ccf_ccf_ID31_ID32_res.pdf’
  ‘output_ENSO_NHSST.tmp’ ‘plot_plot_ts_RAW_BIN_enso_sst.pdf’
  ‘plot_plot_ts_RAW_BIN_enso_sst01.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst02.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst03.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst04.png’ ‘plot_ts_ACER_ABRUPT.pdf’
  ‘plot_ts_ACER_ABRUPT01.png’ ‘plot_ts_ACER_ABRUPT02.png’
  ‘plot_ts_ACER_ABRUPT03.png’ ‘plot_ts_ACER_ABRUPT04.png’
  ‘salida_ACER_ABRUPT.tmp’ ‘scaterplot_scatterplot_ENSO_SST.jpg’
  ‘scaterplot_scatterplot_ENSO_SST.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
bin_ps: no visible global function definition for ‘runif’
bin_ps: no visible global function definition for ‘dbinom’
draw_i: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbinom runif
Consider adding
  importFrom("stats", "dbinom", "runif")
to your NAMESPACE file.
IndivdRUMIndMH: no visible global function definition for
  ‘flush.console’
dRUMAuxMix: no visible global function definition for ‘flush.console’
dRUMHAM: no visible global function definition for ‘flush.console’
dRUMIndMH: no visible global function definition for ‘flush.console’
print.binomlogit: no visible global function definition for ‘is’
summary.binomlogit: no visible global function definition for ‘is’
Undefined global functions or variables:
  flush.console is
Consider adding
  importFrom("methods", "is")
  importFrom("utils", "flush.console")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls in package code:
  ‘ggplot2’ ‘lattice’ ‘polynom’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested 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.
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
bins.quantiles: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘msa’
Running ‘testthat.R’ [20s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("bio3d")
  Loading required package: bio3d
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (29)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-fitting.R:22:3): Fitting still works ────────────────────────────
  Error in `rmsd(pdbs)`: No comparison can be made, input was only a single vector 'a'
  Backtrace:
      █
   1. ├─testthat::expect_that(...) test-fitting.R:22:2
   2. │ └─testthat:::condition(object)
   3. │   └─testthat::expect_equal(x, expected, ..., expected.label = label)
   4. │     └─testthat::quasi_label(enquo(object), label, arg = "object")
   5. │       └─rlang::eval_bare(expr, quo_get_env(quo))
   6. ├─base::suppressWarnings(rmsd(pdbs))
   7. │ └─base::withCallingHandlers(...)
   8. └─bio3d::rmsd(pdbs)
  
  [ FAIL 1 | WARN 0 | SKIP 29 | PASS 167 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Found the following files/directories:
  ‘Plots.pdf’
Found the following files/directories:
  ‘pointshape.dbf’ ‘pointshape.shp’ ‘pointshape.shx’
Running examples in ‘biogrowth-Ex.R’ failed
The error most likely occurred in:

> ### Name: fit_isothermal_growth
> ### Title: Fit primary growth models
> ### Aliases: fit_isothermal_growth
> 
> ### ** Examples
> 
> 
> ## Some dummy data
> 
> library(tibble)
> 
> my_data <- tibble(time = c(0, 25, 50, 75, 100),
+     logN = c(2, 2.5, 7, 8, 8))
> 
> ## Choose the model
> 
> my_model <- "Baranyi"
> 
> ## Initial values for the model parameters
> 
> start = c(logNmax = 8, lambda = 25, logN0 = 2)
> 
> ## Any model parameter can be fixed
> 
> known <- c(mu = .2)
> 
> ## Now, we can call the function
> 
> static_fit <- fit_isothermal_growth(my_data, my_model, start, known)
Error in xy.coords(x, y, setLab = FALSE) : 
  'list' object cannot be coerced to type 'double'
Calls: fit_isothermal_growth ... modCost -> approx -> regularize.values -> xy.coords
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Publication-ready-figures-with-biogrowth.Rmd’ using rmarkdown
Quitting from lines 130-142 (Publication-ready-figures-with-biogrowth.Rmd) 
Error: processing vignette 'Publication-ready-figures-with-biogrowth.Rmd' failed with diagnostics:
'list' object cannot be coerced to type 'double'
--- failed re-building ‘Publication-ready-figures-with-biogrowth.Rmd’

--- re-building ‘biogrowth_basics.Rmd’ using rmarkdown
Quitting from lines 680-684 (biogrowth_basics.Rmd) 
Error: processing vignette 'biogrowth_basics.Rmd' failed with diagnostics:
'list' object cannot be coerced to type 'double'
--- failed re-building ‘biogrowth_basics.Rmd’

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

SUMMARY: processing the following files failed:
  ‘Publication-ready-figures-with-biogrowth.Rmd’ ‘biogrowth_basics.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘inactivation.Rmd’ using rmarkdown
Quitting from lines 665-668 (inactivation.Rmd) 
Error: processing vignette 'inactivation.Rmd' failed with diagnostics:
'list' object cannot be coerced to type 'double'
--- failed re-building ‘inactivation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘desc’ ‘lme4’ ‘mitml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘spatstat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘fs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
'library' or 'require' call to ‘MGRASTer’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for ‘packageVersion’
biom.matrix: no visible global function definition for ‘packageVersion’
Undefined global functions or variables:
  packageVersion
Consider adding
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Running examples in ‘bioOED-Ex.R’ failed
The error most likely occurred in:

> ### Name: calculate_pars_correlation
> ### Title: Correlation Between Model Parameters Sensitivities
> ### Aliases: calculate_pars_correlation
> 
> ### ** Examples
> 
> 
> parms_fix <- c(temp_ref = 57.5)
> parms <- c(delta_ref = 3.9, z = 4.2, p = 1, N0 = 1e6)
> temp_profile <- data.frame(time = c(0, 60), temperature = c(30, 60))
> correlations <- calculate_pars_correlation("Mafart", parms,
+                                             temp_profile, parms_fix)
Warning: `mutate_()` was deprecated in dplyr 0.7.0.
Please use `mutate()` instead.
See vignette('programming') for more help
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
Error in Sens[, i] <- (yPert - yRef)/dp[i] * parscale[i]/varscale : 
  incorrect number of subscripts on matrix
Calls: calculate_pars_correlation -> sensitivity_inactivation -> sensFun
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘vignette_bioOED.Rmd’ using rmarkdown
Quitting from lines 100-103 (vignette_bioOED.Rmd) 
Error: processing vignette 'vignette_bioOED.Rmd' failed with diagnostics:
incorrect number of subscripts on matrix
--- failed re-building ‘vignette_bioOED.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
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.
'LazyData' is specified without a 'data' directory
Note: found 46 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘magrittr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
biwt.cor: no visible global function definition for ‘covMcd’
biwt.cor: no visible binding for global variable ‘mad’
biwt.est: no visible global function definition for ‘covMcd’
biwt.est: no visible global function definition for ‘mahalanobis’
chi.int: no visible global function definition for ‘pchisq’
chi.int.p: no visible global function definition for ‘dchisq’
chi.int2: no visible global function definition for ‘pchisq’
chi.int2.p: no visible global function definition for ‘dchisq’
rejpt.bw: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  covMcd dchisq mad mahalanobis pchisq
Consider adding
  importFrom("stats", "dchisq", "mad", "mahalanobis", "pchisq")
to your NAMESPACE file.
Package suggested but not available for checking: ‘RQuantLib’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘blackbox-Ex.R’ failed
The error most likely occurred in:

> ### Name: bboptim
> ### Title: Black-box function optimization
> ### Aliases: bboptim rbb
> ### Keywords: optimize
> 
> ### ** Examples
> 
> # Classical toy example with optional noise
> fr <- function(v,sd) {   ## Rosenbrock Banana function 
+   10 * (v["y"] - v["x"]^2)^2 + (1 - v["x"])^2 + rnorm(1,sd=sd)
+ }
> set.seed(123)
> 
> # Initial parameter values, including duplicates. See ?init_grid.
> parsp <- init_grid(lower=c(x=0,y=0),upper=c(x=2,y=2),nUnique=25)
> 
> #### Without noise
> # add function values
> simuls <- cbind(parsp,bb=apply(parsp,1,"fr",sd=0))
> 
> # optimization
> bbresu <- bboptim(simuls)
    Only 25 unique coordinates selected for cross-validation.
Error in .get_locdata(newdata, locform = locform, object = object, variances = variances) : 
  (!) newdata has incorrect length. It should match the following variables:
 x y
Calls: bboptim ... predict.HLfit -> .predict_body -> .calc_new_X_ZAC -> .get_locdata
Execution halted
Namespaces in Imports field not imported from:
  ‘R6’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Running examples in ‘blink-Ex.R’ failed
The error most likely occurred in:

> ### Name: rl.gibbs
> ### Title: Gibbs sampler for empirically motivated Bayesian record linkage
> ### Aliases: rl.gibbs
> 
> ### ** Examples
> 
> data(RLdata500)
> X.c <- as.matrix(RLdata500[c("by","bm","bd")])[1:3,]
> p.c <- ncol(X.c)
> X.s <- as.matrix(RLdata500[c(1,3)])[1:3,]
> p.s <- ncol(X.s)
> file.num <- rep(c(1,1,1),c(1,1,1))
> d <- function(string1,string2){adist(string1,string2)}
> lam.gs <- rl.gibbs(file.num,X.s,X.c,num.gs=2,a=.01,b=100,c=1,d, M=3)
[1] "Gibbs sampler iteration 1"
[1] "     Drawing beta"
[1] "     Drawing z"
Warning in `[.data.frame`(x$env$data, 1L, drop = FALSE) :
  'drop' argument will be ignored
Warning in `[.data.frame`(x$env$data, 2L, drop = FALSE) :
  'drop' argument will be ignored
Error in alpha[[l]] : recursive indexing failed at level 2
Calls: rl.gibbs ... loop_apply -> <Anonymous> -> .fun -> do.call -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘introEBLink.Rmd’ using rmarkdown
Loading required package: stringdist
Loading required package: plyr
Quitting from lines 91-98 (introEBLink.Rmd) 
Error: processing vignette 'introEBLink.Rmd' failed with diagnostics:
recursive indexing failed at level 2

--- failed re-building ‘introEBLink.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
blockMessage : <anonymous>: no visible global function definition for
  ‘head’
blockMessage: no visible global function definition for ‘head’
blockMessage: no visible global function definition for ‘tail’
Undefined global functions or variables:
  head tail
Consider adding
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
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.
Found the following files/directories:
  ‘Groupa.csv’ ‘Groupa.tex’ ‘Groupb.csv’ ‘Groupb.tex’ ‘Groupc.csv’
  ‘Groupc.tex’ ‘file1.csv’ ‘file1.tex’ ‘file2.csv’ ‘file2.tex’
  ‘file3.csv’ ‘file3.tex’
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘ggplot2’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘ggplot2’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  ‘coda’ ‘functional’ ‘plyr’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘coda’ ‘functional’ ‘plyr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HDistNoSize: no visible global function definition for ‘density’
HDistSize: no visible global function definition for ‘density’
bmkconverge: no visible global function definition for ‘Compose’
bmksensitive: no visible global function definition for ‘Compose’
bmksummary: no visible global function definition for ‘Compose’
bmksummary: no visible global function definition for ‘Curry’
bmksummary: no visible binding for global variable ‘quantile’
bmksummary : std.error: no visible global function definition for ‘var’
bmksummary: no visible global function definition for ‘mcmc’
bmksummary: no visible global function definition for ‘mcmc.list’
bmksummary: no visible global function definition for ‘median’
bmksummary: no visible global function definition for ‘effectiveSize’
bmksummary: no visible global function definition for ‘gelman.diag’
Undefined global functions or variables:
  Compose Curry density effectiveSize gelman.diag mcmc mcmc.list median
  quantile var
Consider adding
  importFrom("stats", "density", "median", "quantile", "var")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
bmmix : LL.y: no visible global function definition for ‘dmultinom’
bmmix : LL.x : <anonymous>: no visible global function definition for
  ‘dmultinom’
bmmix : LPrior.alpha: no visible global function definition for ‘dexp’
bmmix : alpha.move: no visible global function definition for ‘rnorm’
bmmix : alpha.move: no visible global function definition for ‘runif’
bmmix : phi.move: no visible global function definition for ‘rnorm’
bmmix : phi.move: no visible global function definition for ‘runif’
bmmix: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  dexp dmultinom read.table rnorm runif
Consider adding
  importFrom("stats", "dexp", "dmultinom", "rnorm", "runif")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘mcmc.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
Namespace in Imports field not imported from: ‘coda’
  All declared Imports should be used.
Running examples in ‘BMS-Ex.R’ failed
The error most likely occurred in:

> ### Name: lps.bma
> ### Title: Log Predictive Score
> ### Aliases: lps.bma
> ### Keywords: utilities
> 
> ### ** Examples
> 
>  data(datafls)
>  mm=bms(datafls,user.int=FALSE,nmodel=100)
>  
>  #LPS for actual values under the used data (static forecast)
>  lps.bma(mm, realized.y=datafls[,1] , newdata=datafls[,-1])
Error in newX - matrix(colMeans(yXdata[, -1, drop = FALSE]), rnew, K,  : 
  non-numeric argument to binary operator
Calls: lps.bma -> pred.density
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘bms.Rnw’ using Sweave

Error: processing vignette 'bms.Rnw' failed with diagnostics:
 chunk 38 
Error in newX - matrix(colMeans(yXdata[, -1, drop = FALSE]), rnew, K,  : 
  non-numeric argument to binary operator

--- failed re-building ‘bms.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
make_topology: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘matrixcalc’
  All declared Imports should be used.
bnlr: no visible global function definition for ‘dnorm’
bnlr: no visible global function definition for ‘runif’
chainsum : <anonymous>: no visible global function definition for
  ‘quantile’
infocrit: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm quantile runif
Consider adding
  importFrom("stats", "dnorm", "quantile", "runif")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘fastDummies’
  All declared Imports should be used.
Running examples in ‘bnpa-Ex.R’ failed
The error most likely occurred in:

> ### Name: create.dummies
> ### Title: Creates dummy variables in the data set and remove master
> ###   variables
> ### Aliases: create.dummies
> 
> ### ** Examples
> 
> # Clean environment
> closeAllConnections()
> rm(list=ls())
> # Set enviroment
> # setwd("to your working directory")
> # Load packages
> library(bnpa)
> # Use working data sets from package
> data(dataQualiN)
> # Show the structure before
> str(dataQualiN)
'data.frame':	500 obs. of  8 variables:
 $ A: Factor w/ 2 levels "no","yes": 1 1 1 1 1 1 1 1 1 1 ...
 $ S: Factor w/ 2 levels "no","yes": 2 2 1 1 1 2 1 2 2 2 ...
 $ T: Factor w/ 2 levels "no","yes": 1 1 2 1 1 1 1 1 1 1 ...
 $ L: Factor w/ 2 levels "no","yes": 1 1 1 1 1 1 1 1 1 1 ...
 $ B: Factor w/ 2 levels "no","yes": 2 1 1 2 1 1 1 2 2 2 ...
 $ E: Factor w/ 2 levels "no","yes": 1 1 2 1 1 1 1 1 1 1 ...
 $ X: Factor w/ 2 levels "no","yes": 1 1 2 1 1 1 1 1 1 1 ...
 $ D: Factor w/ 2 levels "no","yes": 2 1 2 2 2 2 1 2 2 2 ...
> # Set possible dummy variables
> dummy.vars <- c("A", "B")
> # Create dummies
> dataQualiN <- bnpa::create.dummies(dataQualiN, dummy.vars)
Error in fastDummies::dummy_cols(data.to.work, select_columns = c("A",  : 
  select_columns is/are not in data. Please check data and spelling.
Calls: <Anonymous> -> eval -> eval -> <Anonymous>
Execution halted
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘e1071’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
BOGest: no visible global function definition for ‘read.table’
BOGstat: no visible global function definition for ‘phyper’
BOGstat: no visible global function definition for ‘wilcox.test’
BOGstat: no visible global function definition for ‘p.adjust’
gseaplot: no visible global function definition for ‘par’
gseaplot: no visible global function definition for ‘points’
gseaplot: no visible global function definition for ‘axis’
gseaplot: no visible global function definition for ‘segments’
hgplot: no visible global function definition for ‘par’
hgplot: no visible global function definition for ‘barplot’
Undefined global functions or variables:
  axis barplot p.adjust par phyper points read.table segments
  wilcox.test
Consider adding
  importFrom("graphics", "axis", "barplot", "par", "points", "segments")
  importFrom("stats", "p.adjust", "phyper", "wilcox.test")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  ‘attractors.tex’ ‘cellcycle.sbml’ ‘cellcycle.txt’ ‘pajek_export.net’
  ‘sequence.txt’ ‘testNet.bn’
Namespace in Imports field not imported from: ‘pryr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘HSAUR3’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
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.
Malformed Description field: should contain one or more complete sentences.
specdens: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Rd file 'specdens.Rd':
  \examples lines wider than 100 characters:
                                                                                         #the first 20 values of the 
                                                                                         #time series Nile and WWWusage

These lines will be truncated in the PDF manual.
boot.stepAIC: no visible global function definition for ‘update’
boot.stepAIC: no visible binding for global variable ‘coef’
boot.stepAIC : <anonymous>: no visible global function definition for
  ‘anova’
boot.stepAIC: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  anova coef pnorm update
Consider adding
  importFrom("stats", "anova", "coef", "pnorm", "update")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
boottol: no visible global function definition for ‘setNames’
boottol : shift: no visible global function definition for ‘tail’
boottol : shift: no visible global function definition for ‘head’
boottol: no visible global function definition for ‘na.omit’
vastol: no visible global function definition for ‘setNames’
vastol: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  head na.omit setNames tail
Consider adding
  importFrom("stats", "na.omit", "setNames")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Rd file 'beq.lin.Rd':
  \examples lines wider than 100 characters:
     plot(x,h_sol0,type="l",lty=1,main=paste("Water Surface Elevetion after",t,"days",sep=" "),xlab="x[m]",ylab="h[m]")

Rd file 'beq.song.Rd':
  \examples lines wider than 100 characters:
     plot(x,h_sol1,type="l",lty=1,main="Water Surface Elevetion (Song at's solution) ",xlab="x[m]",ylab="h[m]")

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1448 marked UTF-8 strings
GNU make is a SystemRequirements.
bPeaksAnalysis: no visible global function definition for ‘write.table’
dataReading: no visible global function definition for ‘read.table’
dataSmoothing: no visible global function definition for ‘filter’
peakDetection: no visible global function definition for ‘quantile’
peakDetection: no visible global function definition for ‘pdf’
peakDetection: no visible global function definition for ‘par’
peakDetection: no visible global function definition for ‘text’
peakDetection: no visible global function definition for ‘abline’
peakDetection: no visible global function definition for ‘points’
peakDetection: no visible global function definition for ‘dev.off’
peakDetection: no visible global function definition for ‘write.table’
peakDrawing: no visible global function definition for ‘par’
peakDrawing: no visible global function definition for ‘abline’
peakLocation: no visible global function definition for ‘read.table’
peakLocation: no visible global function definition for ‘pdf’
peakLocation: no visible global function definition for ‘barplot’
peakLocation: no visible global function definition for ‘dev.off’
peakLocation: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  abline barplot dev.off filter par pdf points quantile read.table text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "barplot", "par", "points", "text")
  importFrom("stats", "filter", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘bPeaks_example-chrIV.bed’ ‘bPeaks_example-chrIV_bPeaksDrawing.pdf’
  ‘bPeaks_example-chrIV_dataSummary.pdf’
  ‘bPeaks_example_bPeaks_allGenome.bed’
  ‘bPeaks_example_bPeaks_parameterSummary.txt’
  ‘bPeaks_example_chrIV.bed’ ‘bPeaks_example_chrIV_bPeaksDrawing.pdf’
  ‘bPeaks_example_chrIV_dataSummary.pdf’
  ‘bPeaks_example_peakLocation.pdf’
  ‘bPeaks_example_peakLocation_inCDS.txt’
  ‘bPeaks_example_peakLocation_inPromoters.txt’ ‘peakStats.Robject’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘CCA’ ‘brainR’ ‘elasticnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
apply.breaks: no visible binding for global variable ‘median’
break.clust: no visible global function definition for ‘median’
breakage.plot: no visible binding for global variable ‘median’
breakage.plot: no visible global function definition for ‘abline’
breakage.plot: no visible global function definition for ‘lm’
find.bottom: no visible global function definition for ‘filter’
fit.breakage: no visible global function definition for ‘optim’
fit.breakage: no visible global function definition for ‘points’
fit.sensitivity.plot: no visible global function definition for
  ‘contour’
fit.sensitivity.plot: no visible global function definition for
  ‘points’
fit.sensitivity.plot: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline contour filter lm median optim points text
Consider adding
  importFrom("graphics", "abline", "contour", "points", "text")
  importFrom("stats", "filter", "lm", "median", "optim")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘breathteststan’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘brew-test-1-1.eps’ ‘brew-test-1-2.eps’ ‘brew-test-1.tex’
  ‘brew-test-2.html’
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘kableExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘profileModel’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cmdstanr’
Package suggested but not available for checking: ‘glmmADMB’
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Running examples in ‘broom-Ex.R’ failed
The error most likely occurred in:

> ### Name: tidy.kde
> ### Title: Tidy a(n) kde object
> ### Aliases: tidy.kde kde_tidiers ks_tidiers
> 
> ### ** Examples
> 
> 
> if (requireNamespace("ks", quietly = TRUE)) {
+ 
+ library(ks)
+ 
+ dat <- replicate(2, rnorm(100))
+ k <- kde(dat)
+ 
+ td <- tidy(k)
+ td
+ 
+ library(ggplot2)
+ library(dplyr)
+ library(tidyr)
+ 
+ td %>%
+   pivot_wider(c(obs, estimate),
+     names_from = variable,
+     values_from = value
+   ) %>%
+   ggplot(aes(x1, x2, fill = estimate)) +
+   geom_tile() +
+   theme_void()
+ 
+ # also works with 3 dimensions
+ dat3 <- replicate(3, rnorm(100))
+ k3 <- kde(dat3)
+ 
+ td3 <- tidy(k3)
+ td3
+ 
+ }
Error in t(x) - mean : non-numeric argument to binary operator
Calls: kde -> kde.grid.2d -> dmvnorm -> backsolve
Execution halted
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rworldxtra’ ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
BSGS.Sample: no visible global function definition for ‘rgamma’
BSGS.Simple: no visible global function definition for ‘rgamma’
CompWiseGibbs: no visible global function definition for ‘runif’
CompWiseGibbs: no visible global function definition for ‘rnorm’
CompWiseGibbsSMP: no visible global function definition for ‘rbinom’
CompWiseGibbsSMP: no visible global function definition for ‘runif’
CompWiseGibbsSMP: no visible global function definition for ‘rnorm’
CompWiseGibbsSimple: no visible global function definition for ‘runif’
CompWiseGibbsSimple: no visible global function definition for ‘rnorm’
CompWiseGibbsSimple: no visible global function definition for ‘rgamma’
GroupMH: no visible global function definition for ‘runif’
GroupZ.MH: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rbinom rgamma rnorm runif
Consider adding
  importFrom("stats", "rbinom", "rgamma", "rnorm", "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
plot.bspec: no visible global function definition for ‘par’
plot.bspec: no visible global function definition for ‘matlines’
plot.bspec: no visible global function definition for ‘points’
plot.bspec: no visible global function definition for ‘axis’
plot.bspec: no visible global function definition for ‘mtext’
plot.bspec: no visible global function definition for ‘axTicks’
plot.bspec: no visible global function definition for ‘box’
plot.bspecACF: no visible global function definition for ‘abline’
plot.bspecACF: no visible global function definition for ‘matlines’
Undefined global functions or variables:
  abline axTicks axis box matlines mtext par points
Consider adding
  importFrom("graphics", "abline", "axTicks", "axis", "box", "matlines",
             "mtext", "par", "points")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘grDevices’ ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mvtnorm’ ‘ssmn’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘magrittr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
alpha.proxy: no visible global function definition for ‘filled.contour’
alpha.proxy: no visible global function definition for ‘axis’
alpha.proxy: no visible global function definition for ‘contour’
factor.model.stat: no visible global function definition for ‘quantile’
factor.model.stat: no visible global function definition for ‘lsfit’
partial.rainbow: no visible binding for global variable ‘rainbow’
var.shrink.eqcor: no visible global function definition for ‘var’
var.shrink.eqcor: no visible global function definition for ‘quantile’
var.shrink.eqcor: no visible global function definition for ‘cov2cor’
Undefined global functions or variables:
  axis contour cov2cor filled.contour lsfit quantile rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "contour", "filled.contour")
  importFrom("stats", "cov2cor", "lsfit", "quantile", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
plot.bursts: no visible global function definition for ‘axis’
plot.bursts: no visible global function definition for ‘arrows’
Undefined global functions or variables:
  arrows axis
Consider adding
  importFrom("graphics", "arrows", "axis")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Rd file 'bvenn.Rd':
  \examples lines wider than 100 characters:
                     bvenn(list(Set1 = sample(letters, 16), Set2 = sample(letters, 3+ 3*j), Set3 = sample(letters, 7)), add = TRUE, fontsize ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Malformed Description field: should contain one or more complete sentences.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
makemim: no visible global function definition for ‘cor’
sigtestMTC: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  cor p.adjust
Consider adding
  importFrom("stats", "cor", "p.adjust")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘qgraph’ ‘reshape2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Running examples in ‘CAinterprTools-Ex.R’ failed
The error most likely occurred in:

> ### Name: caScatter
> ### Title: Scatterplot visualization facility
> ### Aliases: caScatter
> ### Keywords: caScatter
> 
> ### ** Examples
> 
> data(greenacre_data)
> 
> # symmetric scatterplot for rows and columns
> caScatter(greenacre_data, 1, 2, type=1) 
Error in CA(X = data, ncp = dimensionality, graph = FALSE) : 
  could not find function "CA"
Calls: caScatter ... as.data.frame -> as.data.frame.list -> do.call -> <Anonymous>
Execution halted
Found the following significant warnings:
  /usr/include/gtk-2.0/gtk/gtktypeutils.h:236:1: warning: ‘GTypeDebugFlags’ is deprecated [-Wdeprecated-declarations]
  /usr/include/gtk-2.0/gtk/gtktooltips.h:73:3: warning: ‘GTimeVal’ is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-devel/cairoDevice.Rcheck/00install.out’ for details.
Output from running autoreconf:
  configure.ac:22: warning: AC_OUTPUT should be used without arguments.
  configure.ac:22: You should run autoupdate.
  configure.ac:22: warning: AC_OUTPUT should be used without arguments.
  configure.ac:22: You should run autoupdate.
---- unloading

 *** caught segfault ***
address 0x7f1f9cab4a90, cause 'invalid permissions'
An irrecoverable exception occurred. R is aborting now ...
File ‘cairoDevice/R/zzz.R’:
  .onLoad calls:
    message("R session is headless; GTK+ not initialized.")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.
File ‘cairoDevice/libs/cairoDevice.so’:
  Found non-API call to R: ‘R_CStackLimit’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Output from running autoreconf:
  configure.ac:4: warning: The macro `AC_CONFIG_HEADER' is obsolete.
  configure.ac:4: You should run autoupdate.
  ./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from...
  configure.ac:4: the top level
  configure.ac:28: warning: The macro `AC_HEADER_STDC' is obsolete.
  configure.ac:28: You should run autoupdate.
  ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from...
  configure.ac:28: the top level
  configure.ac:4: warning: The macro `AC_CONFIG_HEADER' is obsolete.
  configure.ac:4: You should run autoupdate.
  ./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from...
  configure.ac:4: the top level
  configure.ac:28: warning: The macro `AC_HEADER_STDC' is obsolete.
  configure.ac:28: You should run autoupdate.
  ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from...
  configure.ac:28: the top level
File ‘Cairo/libs/Cairo.so’:
  Found non-API calls to R: ‘R_InputHandlers’, ‘addInputHandler’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
Running examples in ‘CalibrateSSB-Ex.R’ failed
The error most likely occurred in:

> ### Name: CalibrateSSB
> ### Title: Calibration weighting and estimation
> ### Aliases: CalibrateSSB
> 
> ### ** Examples
> 
> 
> # Generates data  - two years
> z    <- AkuData(3000)  # 3000 in each quarter
> zPop <- AkuData(10000)[,1:7]
> 
> # Calibration using "survey"
> a <- CalibrateSSB(z, calmodel = "~ sex*age",
+                  partition = c("year","q"),  # calibrate within quarter
+                  popData = zPop, y = c("unemployed","workforce"),
+                  by = c("year","q")) # Estimate within quarter
> head(a$w) # calibrated weights
[1] 3.964029 3.989130 3.964029 0.000000 3.964029 3.881720
> a$estTM   # estimates
  year q unemployed workforce
1 2014 1   225.8183  7172.557
3 2014 2   278.3538  7302.205
5 2014 3   206.2096  7304.658
7 2014 4   188.6045  7276.304
2 2015 1   187.0663  7246.500
4 2015 2   209.8814  7226.914
6 2015 3   191.8178  7166.970
8 2015 4   223.4013  7214.363
> a$popTotals   # popTotals used as input below
  year q (Intercept) sex1 age2 age3 sex1:age2 sex1:age3
1 2014 1       10000 5033 4370 2758      2166      1399
2 2014 2       10000 5049 4372 2667      2182      1352
3 2014 3       10000 5060 4368 2646      2195      1337
4 2014 4       10000 5055 4349 2596      2192      1302
5 2015 1       10000 5030 4379 2716      2216      1360
6 2015 2       10000 5017 4392 2643      2219      1323
7 2015 3       10000 5042 4389 2584      2226      1299
8 2015 4       10000 5055 4377 2531      2217      1287
> 
> 
> # Calibration, no package, popTotals as input
> b <- CalibrateSSB(z, popTotals=a$popTotals, calmodel="~ sex*age",
+       partition = c("year","q"), usePackage = "none", y = c("unemployed","workforce"))
Error in data[, mfCalNames[okNames], drop = FALSE] : 
  incorrect number of dimensions
Calls: CalibrateSSB -> calibrateSSB -> lagVekter -> getTotal -> cbind
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(CalibrateSSB)
  Loading required package: survey
  Loading required package: grid
  Loading required package: Matrix
  Loading required package: survival
  
  Attaching package: 'survey'
  
  The following object is masked from 'package:graphics':
  
      dotchart
  
  > 
  > test_check("CalibrateSSB")
  Error in h(simpleError(msg, call)) : 
    error in evaluating the argument 'b' in selecting a method for function 'solve': non-numeric argument to binary operator
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-CalibrateSSB.R:44:3): Examples ──────────────────────────────────
  Error in `data[, mfCalNames[okNames], drop = FALSE]`: incorrect number of dimensions
  Backtrace:
      █
   1. └─CalibrateSSB::CalibrateSSB(...) test-CalibrateSSB.R:44:2
   2.   └─CalibrateSSB:::calibrateSSB(...)
   3.     └─CalibrateSSB:::lagVekter(...)
   4.       └─CalibrateSSB:::getTotal(pop, lm_modell)
   5.         └─base::cbind(...)
  ── Error (test-CalibrateSSB.R:107:3): samplingWeights ──────────────────────────
  Error in `calibratePackageSurvey(grossSample = grossSample, modelformula = calModel, 
      popTotals = popTotals, response = response, popData = popData, 
      samplingWeights = w, bounds = bounds, calfun = calfun, totalReturn = totalReturn, 
      returnwGross = TRUE, ...)`: The function calibrate in package survey did not succeed. Maybe change the parameter usePackage?
  Backtrace:
      █
   1. └─CalibrateSSB::CalibrateSSB(...) test-CalibrateSSB.R:107:2
   2.   └─CalibrateSSB:::calibrateSSB(...)
   3.     └─CalibrateSSB:::calibratePackageSurvey(...)
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 6 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Running ‘spelling.R’
  Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(campfin)
  > 
  > test_check("campfin")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (5)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-normal-phone.R:45:3): normal phone stops on bad input ─────────
  `normal_phone(mtcars)` did not throw an error.
  
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 165 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Note: found 287 marked UTF-8 strings
Note: found 23 marked UTF-8 strings
Found the following files/directories:
  ‘tmp.txt’
Found the following files/directories:
  ‘MDA231_tree.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 59 marked UTF-8 strings
Running examples in ‘capm-Ex.R’ failed
The error most likely occurred in:

> ### Name: CalculateGlobalSens
> ### Title: Global sensitivity analysis
> ### Aliases: CalculateGlobalSens
> 
> ### ** Examples
> 
> ## IASA model
> 
> ## Parameters and intial conditions.
> data(dogs)
> dogs_iasa <- GetDataIASA(dogs,
+                          destination.label = "Pinhais",
+                          total.estimate = 50444)
> 
> # Solve for point estimates.
> solve_iasa_pt <- SolveIASA(pars = dogs_iasa$pars,
+                           init = dogs_iasa$init,
+                           time = 0:15,
+                           alpha.owned = TRUE,
+                           method = 'rk4')
> 
> ## Set ranges 10 % greater and lesser than the
> ## point estimates.
> rg_solve_iasa <- SetRanges(pars = dogs_iasa$pars)
> 
> ## Calculate golobal sensitivity of combined parameters.
> ## To calculate global sensitivity to each parameter, set
> ## all as FALSE.
> glob_all_solve_iasa <- CalculateGlobalSens(
+   model.out = solve_iasa_pt,
+   ranges = rg_solve_iasa, 
+   sensv = "n2", all = TRUE)
Warning in ii * dpar :
  longer object length is not a multiple of shorter object length
Warning in rr * dpar :
  longer object length is not a multiple of shorter object length
Error in if (f1 + fs1 + m1 + ms1 <= k1) { : 
  missing value where TRUE/FALSE needed
Calls: CalculateGlobalSens ... <Anonymous> -> func -> with -> with.default -> eval -> eval
Execution halted
Namespaces in Imports field not imported from:
  ‘htmltools’ ‘shinydashboard’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
bootstrapCapwire: no visible global function definition for ‘quantile’
drawCapRatesBeta : <anonymous>: no visible global function definition
  for ‘rbeta’
drawCapRatesExp : <anonymous>: no visible global function definition
  for ‘rexp’
drawCapRatesGamma : <anonymous>: no visible global function definition
  for ‘rgamma’
drawCapRatesGeom : <anonymous>: no visible global function definition
  for ‘rgeom’
drawCapRatesUnif : <anonymous>: no visible global function definition
  for ‘runif’
partitionCountData : find.3.way.partitions: no visible global function
  definition for ‘dmultinom’
Undefined global functions or variables:
  dmultinom quantile rbeta rexp rgamma rgeom runif
Consider adding
  importFrom("stats", "dmultinom", "quantile", "rbeta", "rexp", "rgamma",
             "rgeom", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘details’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘methods’ ‘readr’ ‘recipes’ ‘sf’ ‘stringr’ ‘utils’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Sub.pair: no visible global function definition for ‘qnorm’
as.record: no visible global function definition for ‘capture.output’
estN: no visible global function definition for ‘sd’
estN: no visible global function definition for ‘qnorm’
estN.bootstrap: no visible global function definition for ‘runif’
Undefined global functions or variables:
  capture.output qnorm runif sd
Consider adding
  importFrom("stats", "qnorm", "runif", "sd")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Running examples in ‘caret-Ex.R’ failed
The error most likely occurred in:

> ### Name: classDist
> ### Title: Compute and predict the distances to class centroids
> ### Aliases: classDist classDist.default predict.classDist
> ### Keywords: manip
> 
> ### ** Examples
> 
> trainSet <- sample(1:150, 100)
> 
> distData <- classDist(iris[trainSet, 1:4],
+                       iris$Species[trainSet])
> 
> newDist <- predict(distData,
+                    iris[-trainSet, 1:4])
Error in FUN(x, aperm(array(STATS, dims[perm]), order(perm)), ...) : 
  non-numeric argument to binary operator
Calls: predict ... predict.classDist -> lapply -> FUN -> mahalanobis -> sweep
Execution halted
Running ‘testthat.R’ [278s/341s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(caret)
  Loading required package: ggplot2
  Loading required package: lattice
  > 
  > test_check("caret")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (33)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_classDist.R:96:3): predictions ──────────────────────────────────
  Error in `FUN(x, aperm(array(STATS, dims[perm]), order(perm)), ...)`: non-numeric argument to binary operator
  Backtrace:
      █
   1. ├─testthat::expect_equal(...) test_classDist.R:96:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─stats::predict(distData, x)
   5. └─caret:::predict.classDist(distData, x)
   6.   └─base::lapply(object$values, pred, x = newdata)
   7.     └─caret:::FUN(X[[i]], ...)
   8.       └─stats::mahalanobis(x, center = a$means, cov = a$A, inverted = TRUE)
   9.         └─base::sweep(x, 2L, center)
  ── Failure (test_ptypes.R:32:3): ptypes for formulas ───────────────────────────
  xy_plain$ptype not equal to `mtcars_0`.
  target is NULL, current is data.frame
  ── Failure (test_ptypes.R:33:3): ptypes for formulas ───────────────────────────
  xy_oned$ptype not equal to `wt_0`.
  target is NULL, current is data.frame
  ── Failure (test_ptypes.R:34:3): ptypes for formulas ───────────────────────────
  xy_dmmy$ptype not equal to `sac_0`.
  target is NULL, current is data.frame
  
  [ FAIL 4 | WARN 0 | SKIP 33 | PASS 150 ]
  Error: Test failures
  Execution halted
abundance: no visible global function definition for ‘D’
Undefined global functions or variables:
  D
Consider adding
  importFrom("stats", "D")
to your NAMESPACE file.
barplotEQR: no visible global function definition for ‘barplot’
barplotEQR: no visible global function definition for ‘abline’
barplotEQR: no visible global function definition for ‘par’
barplotEQR: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline barplot par text
Consider adding
  importFrom("graphics", "abline", "barplot", "par", "text")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'library' or 'require' calls in package code:
  ‘MASS’ ‘RSQLite’ ‘grid’ ‘sm’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following files/directories:
  ‘foo.tab’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘janitor’ ‘tibble’
  All declared Imports should be used.
Note: found 75 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘GAMBoost’
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.
'LazyData' is specified without a 'data' directory
MDR.high.forward1: no visible global function definition for ‘combn’
MDR.sing.mod1: no visible global function definition for ‘combn’
MDR.sing.mod1: no visible global function definition for
  ‘complete.cases’
MDR.sing.mod1: no visible global function definition for ‘lm’
MDR.sing.mod1: no visible global function definition for ‘aov’
MDR.sing.mod1: no visible global function definition for ‘anova’
MDR.stage.forward1: no visible global function definition for ‘combn’
MDR.stage.forward1: no visible global function definition for
  ‘complete.cases’
MDR.stage.forward1: no visible global function definition for ‘lm’
MDR.stage.forward1: no visible global function definition for ‘resid’
MDR.stage.forward1: no visible global function definition for ‘pf’
MDR_forward1: no visible global function definition for
  ‘complete.cases’
MDR_forward1: no visible global function definition for ‘lm’
MDR_forward1: no visible global function definition for ‘aov’
low.anova: no visible global function definition for ‘complete.cases’
low.anova: no visible global function definition for ‘lm’
sing.mod1: no visible global function definition for ‘combn’
sing.mod1: no visible global function definition for ‘complete.cases’
sing.mod1: no visible global function definition for ‘lm’
sing.mod1: no visible global function definition for ‘pf’
Undefined global functions or variables:
  anova aov combn complete.cases lm pf resid
Consider adding
  importFrom("stats", "anova", "aov", "complete.cases", "lm", "pf",
             "resid")
  importFrom("utils", "combn")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘broom’ ‘epitools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spacodiR’
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.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tidyverse’
  All declared Imports should be used.
Found the following files/directories:
  ‘catmapdata.fixed.effects.plot.pdf’ ‘catmapdata.funnel.plot.pdf’
  ‘catmapdata.output.txt’ ‘catmapdata.random.effects.plot.pdf’
Error(s) in re-building vignettes:
--- re-building ‘catnet.Rnw’ using Sweave

Error: processing vignette 'catnet.Rnw' failed with diagnostics:
 chunk 20 (label = ex21) 
Error in cnSamples(cn, numsamples, pert, as.index = TRUE) : 
  'list' object cannot be coerced to type 'integer'

--- failed re-building ‘catnet.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
mi.inference: no visible binding for global variable ‘var’
mi.inference: no visible global function definition for ‘qt’
mi.inference: no visible global function definition for ‘pt’
Undefined global functions or variables:
  pt qt var
Consider adding
  importFrom("stats", "pt", "qt", "var")
to your NAMESPACE file.
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.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
ctab: no visible global function definition for ‘xtabs’
mob.eqmain: no visible global function definition for ‘model.matrix’
mob.qi: no visible global function definition for ‘C’
mob.qi: no visible binding for global variable ‘contr.treatment’
mob.rc1: no visible global function definition for ‘C’
mob.rc1: no visible binding for global variable ‘contr.treatment’
mob.rc1: no visible global function definition for ‘model.matrix’
mob.symint: no visible global function definition for ‘model.matrix’
print.ctab: no visible global function definition for ‘ftable’
Undefined global functions or variables:
  C contr.treatment ftable model.matrix xtabs
Consider adding
  importFrom("stats", "C", "contr.treatment", "ftable", "model.matrix",
             "xtabs")
to your NAMESPACE file.
Rd file 'ctab.Rd':
  \usage lines wider than 90 characters:
     ctab(...,dec.places=NULL,digits=NULL,type=NULL,style=NULL,row.vars=NULL,col.vars=NULL,percentages=NULL,addmargins=NULL)

Rd file 'sqtab.Rd':
  \examples lines wider than 100 characters:
     OccFather<-gl(5,5,labels=c("Upper nonmanual","Lower nonmanual","Upper manual","Lower manual","Farm"))
     glm.q0<-glm(Freq~OccFather+OccSon+mob.qi(OccFather,OccSon,constrained=TRUE),family=poisson(),data=FHtab)
     glm.hrc1<-glm(Freq~OccFather+OccSon+mob.rc1(OccFather,OccSon,equal=TRUE),family=poisson(),data=FHtab)
     m2 <- mlogit(occupation ~ mob.qi(focc,alt)+mob.unif(focc,alt) | education+race,data=pc, reflevel = "farm")

These lines will be truncated in the PDF manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 32 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘CBPS’ ‘spelling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
--- re-building ‘causalsens.Rnw’ using knitr
Error: processing vignette 'causalsens.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'causalsens.tex' failed.
LaTeX errors:
! Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package xcolor Error: Undefined color `fgcolor'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
--- failed re-building ‘causalsens.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘prettydoc’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
ccd.sequential: no visible global function definition for ‘qchisq’
dominate.random.sample: no visible global function definition for
  ‘runif’
draw.circle: no visible global function definition for ‘polygon’
juggle2: no visible global function definition for ‘rbinom’
plot.cccd: no visible global function definition for ‘gray’
plot.cccd: no visible global function definition for ‘points’
plot.cccdClassifier: no visible global function definition for ‘points’
Undefined global functions or variables:
  gray points polygon qchisq rbinom runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "points", "polygon")
  importFrom("stats", "qchisq", "rbinom", "runif")
to your NAMESPACE file.
VD: no visible binding for global variable ‘var’
stratcc : <anonymous>: no visible global function definition for
  ‘hclust’
stratcc : <anonymous>: no visible global function definition for
  ‘cutree’
Undefined global functions or variables:
  cutree hclust var
Consider adding
  importFrom("stats", "cutree", "hclust", "var")
to your NAMESPACE file.
Rd file 'stratcc.Rd':
  \usage lines wider than 90 characters:
     stratcc(x, groups, alloc = "Pro", fraction = 0.1, clustering = FALSE, cluster_method = "ward")

These lines will be truncated in the PDF manual.
Namespace in Imports field not imported from: ‘statmod’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘GeneNet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
p.Roy: no visible global function definition for ‘pf’
p.asym: no visible global function definition for ‘pf’
p.perm: no visible global function definition for ‘cancor’
plt.asym: no visible global function definition for ‘qf’
plt.asym: no visible global function definition for ‘df’
plt.asym: no visible global function definition for ‘abline’
plt.perm: no visible global function definition for ‘hist’
plt.perm: no visible global function definition for ‘mtext’
plt.perm: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline cancor df hist mtext pf qf
Consider adding
  importFrom("graphics", "abline", "hist", "mtext")
  importFrom("stats", "cancor", "df", "pf", "qf")
to your NAMESPACE file.
Rd file 'p.perm.Rd':
  \examples lines wider than 100 characters:
     ## Run permutation test using Wilks Lambda (default) as test statistic; include different numbers of canonical correlations:

Rd file 'plt.asym.Rd':
  \examples lines wider than 100 characters:
     ## Plot the F-approximation for the Hotelling-Lawley Trace, considering 3, 2, or 1 canonical correlation(s):

Rd file 'plt.perm.Rd':
  \examples lines wider than 100 characters:
     # plot the permutation distribution of an F approximation for Wilks' Lambda, considering 3 and 2 canonical correlations:
     # plot the permutation distribution of an F approximation for the Pillai-Bartlett Trace, considering 3, 2, and 1 canonical correlation( ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘fields’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘hotcold.csv’
Namespace in Imports field not imported from: ‘formula.tools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘bitops’ which was already attached by Depends.
  Please remove these calls from your code.
Found the following files/directories:
  ‘Base.txt’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
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.
Namespace in Imports field not imported from: ‘urltools’
  All declared Imports should be used.
Found the following files/directories:
  ‘out.png’ ‘out1.txt’ ‘out2.txt’
Namespaces in Imports field not imported from:
  ‘ggpubr’ ‘matrixStats’ ‘qlcMatrix’
  All declared Imports should be used.
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.
Note: found 907 marked UTF-8 strings
Found the following files/directories:
  ‘figure01ceg.pdf’ ‘figure02ceg.pdf’ ‘staged.tree.graph.pdf’
  ‘stratified-event-tree-plot.pdf’
'LazyData' is specified without a 'data' directory
Packages in Depends field not imported from:
  ‘gplots’ ‘minpack.lm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
erf: no visible global function definition for ‘pnorm’
fitVolDist: no visible global function definition for ‘nls.lm’
fitVolDist: no visible global function definition for ‘nls.lm.control’
fitVolDist: no visible global function definition for ‘optim’
fitVolDist: no visible global function definition for ‘relist’
print.fitVolDist: no visible global function definition for ‘coef’
print.fitVolDist: no visible global function definition for ‘deviance’
print.fitVolDist: no visible global function definition for ‘pt’
print.fitVolDist: no visible global function definition for
  ‘printCoefmat’
resFunChiSq: no visible global function definition for ‘relist’
volEq7: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  coef deviance integrate nls.lm nls.lm.control optim pnorm
  printCoefmat pt relist
Consider adding
  importFrom("stats", "coef", "deviance", "integrate", "optim", "pnorm",
             "printCoefmat", "pt")
  importFrom("utils", "relist")
to your NAMESPACE file.
Error(s) in re-building vignettes:
--- re-building ‘DDC_examples.Rmd’ using knitr
Loading required package: ggplot2
Loading required package: perry
Loading required package: parallel
Loading required package: robustbase
Scalable Robust Estimators with High Breakdown Point (version 1.6-0)


Attaching package: 'rrcov'

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

    getScale

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

--- re-building ‘DI_examples.Rmd’ using knitr
--- finished re-building ‘DI_examples.Rmd’

--- re-building ‘MacroPCA_examples.Rmd’ using knitr
--- finished re-building ‘MacroPCA_examples.Rmd’

--- re-building ‘transfo_examples.Rmd’ using knitr
--- finished re-building ‘transfo_examples.Rmd’

--- re-building ‘wrap_examples.Rmd’ using knitr
Quitting from lines 30-83 (wrap_examples.Rmd) 
Error: processing vignette 'wrap_examples.Rmd' failed with diagnostics:
The arguments "locX" and "scaleX" should both be of length 1
--- failed re-building ‘wrap_examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
cenNID: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
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.
Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
Malformed Description field: should contain one or more complete sentences.
MomNIT: no visible global function definition for ‘dnorm’
MomNIT: no visible global function definition for ‘pnorm’
cdfNI: no visible global function definition for ‘pnorm’
cdfNI: no visible global function definition for ‘pt’
em.cens: no visible global function definition for ‘lm’
em.cens: no visible global function definition for ‘coefficients’
em.cens : ft: no visible global function definition for ‘dt’
em.cens : ft: no visible global function definition for ‘pt’
em.cens: no visible global function definition for ‘optimize’
em.cens: no visible global function definition for ‘dnorm’
em.cens: no visible global function definition for ‘pnorm’
em.cens: no visible global function definition for ‘sd’
Undefined global functions or variables:
  coefficients dnorm dt lm optimize pnorm pt sd
Consider adding
  importFrom("stats", "coefficients", "dnorm", "dt", "lm", "optimize",
             "pnorm", "pt", "sd")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 104 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘alr3’
select_lambda: no visible global function definition for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘base’ ‘stats’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lmtest’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘xgboost’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
cf_estimate_quantiles: no visible global function definition for
  ‘qnorm’
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
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.
'LazyData' is specified without a 'data' directory
Running examples in ‘cglasso-Ex.R’ failed
The error most likely occurred in:

> ### Name: Example
> ### Title: Simulated data for the cglasso vignette
> ### Aliases: Example MKMEP.Sim MM.Sim
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data("Example")
> 
> MM.Sim <- datacggm(Y = MM.Sim$Y, up = 40, X = MM.Sim$X)
Error in datacggm(Y = MM.Sim$Y, up = 40, X = MM.Sim$X) : 
  ‘X’ and ‘Y’ have a different number of rows
Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
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.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘bench’ ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘AER’ ‘graphics’ ‘lmtest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Hartree2Joule: no visible binding for global variable
  ‘universalConstants’
Hertz2Joule: no visible binding for global variable
  ‘universalConstants’
Joule2Hartree: no visible binding for global variable
  ‘universalConstants’
Joule2Hertz: no visible binding for global variable
  ‘universalConstants’
Joule2Kelvin: no visible binding for global variable
  ‘universalConstants’
Joule2centimeterMinusOne: no visible binding for global variable
  ‘universalConstants’
Joule2electronVolt: no visible binding for global variable
  ‘universalConstants’
Joule2kiloCaloriePerMole: no visible binding for global variable
  ‘universalConstants’
Joule2kiloJoulePerMole: no visible binding for global variable
  ‘universalConstants’
KMC: no visible global function definition for ‘runif’
Kelvin2Joule: no visible binding for global variable
  ‘universalConstants’
LandauZener: no visible binding for global variable
  ‘universalConstants’
LandauZenerProbability: no visible binding for global variable
  ‘universalConstants’
Marcus: no visible binding for global variable ‘universalConstants’
MarcusLevichJortner: no visible binding for global variable
  ‘universalConstants’
centimeterMinusOne2Joule: no visible binding for global variable
  ‘universalConstants’
electronVolt2Joule: no visible binding for global variable
  ‘universalConstants’
kiloCaloriePerMole2Joule: no visible binding for global variable
  ‘universalConstants’
kiloJoulePerMole2Joule: no visible binding for global variable
  ‘universalConstants’
Undefined global functions or variables:
  runif universalConstants
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
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.
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘RCurl’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RCurl’ ‘bitops’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createDataset: no visible global function definition for ‘read.csv’
createInventory: no visible global function definition for ‘read.csv’
downloadMaster: no visible global function definition for
  ‘getURLContent’
downloadMaster: no visible global function definition for ‘read.csv’
downloadMaster: no visible global function definition for ‘write.csv’
getMissingScrape: no visible global function definition for ‘read.csv’
readLocalMaster: no visible global function definition for ‘read.csv’
readMonthlyCsv: no visible global function definition for ‘read.csv’
scrapeToCsv: no visible global function definition for ‘download.file’
writeData: no visible global function definition for ‘write.csv’
writeGhcn: no visible global function definition for ‘write.table’
writeInventory: no visible global function definition for ‘write.table’
writeMonthlyStations: no visible global function definition for
  ‘read.csv’
writeMonthlyStations: no visible global function definition for
  ‘write.csv’
Undefined global functions or variables:
  download.file getURLContent read.csv write.csv write.table
Consider adding
  importFrom("utils", "download.file", "read.csv", "write.csv",
             "write.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rappdirs’ ‘stringr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Rd file 'chebR.Rd':
  \examples lines wider than 100 characters:
     return(list(coefs=rlist$xx[1:n],resids=rlist$bb[1:m],rank=rlist$rank,iter=rlist$iter,ocode=rlist$ocode))

These lines will be truncated in the PDF 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.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Running ‘test-all.R’ [22s/27s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("checkmate")
  Loading required package: checkmate
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_checkVector.R:49:3): checkVector ──────────────────────────────
  vlapply(li, is.vector) not equal to vlapply(li, testVector, strict = TRUE).
  1 element mismatch
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 2900 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘stepres00.txt’
Running examples in ‘ChemoSpec-Ex.R’ failed
The error most likely occurred in:

> ### Name: hmapSpectra
> ### Title: Seriated Heat Map for a Spectra Object
> ### Aliases: hmapSpectra
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> 
> data(SrE.IR)
> 
> # Let's look just at the carbonyl region
> IR <- removeFreq(SrE.IR, rem.freq = SrE.IR$freq > 1775 | SrE.IR$freq < 1660)
> p <- plotSpectra(IR, which = 1:16, lab.pos = 1800)
> 
> # Defaults, except for color scheme:
> res <- hmapSpectra(IR, col = heat.colors(5))
Error in ser_permutation_vector(order, method = method$name) : 
  'list' object cannot be coerced to type 'integer'
Calls: hmapSpectra ... seriate.dist -> ser_permutation -> ser_permutation_vector
Execution halted
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘generics’
  All declared Imports should be used.
Package suggested but not available for checking: ‘countreg’
Namespaces in Imports field not imported from:
  'knitr' 'rmarkdown'
  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.
Note: found 29 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 8119 marked UTF-8 strings
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.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
choicemodelr : drawDelta: no visible global function definition for
  ‘rnorm’
choicemodelr : mnlRwMetropOnce: no visible global function definition
  for ‘rnorm’
choicemodelr : mnlRwMetropOnce: no visible global function definition
  for ‘runif’
choicemodelr : rmultireg: no visible global function definition for
  ‘rnorm’
choicemodelr : rwishart: no visible global function definition for
  ‘rchisq’
choicemodelr : rwishart: no visible global function definition for
  ‘rnorm’
choicemodelr : fsh: no visible global function definition for
  ‘flush.console’
choicemodelr: no visible global function definition for ‘matplot’
choicemodelr: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  flush.console matplot rchisq rnorm runif write.table
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "rchisq", "rnorm", "runif")
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
Rd file 'choicemodelr.Rd':
  \examples lines wider than 100 characters:
     estbetas = cbind(estbetas[,1:4],0-apply(estbetas[,1:4],1,sum),estbetas[,5:6],0-apply(estbetas[,5:6],1,sum))
     estbetas = cbind(estbetas[,1:4],0-apply(estbetas[,1:4],1,sum),estbetas[,5:6],0-apply(estbetas[,5:6],1,sum))

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘RBetas.csv’ ‘RLog.txt’ ‘restart.txt’
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Qh.times.dhyper: no visible global function definition for ‘var’
Qh.times.dhyper: no visible global function definition for ‘pnorm’
Qh.times.dhyper: no visible global function definition for ‘dhyper’
TDiM: no visible global function definition for ‘sd’
choplump.default: no visible global function definition for
  ‘flush.console’
choplump.formula: no visible global function definition for ‘terms’
cm.compact: no visible global function definition for ‘dhyper’
Undefined global functions or variables:
  dhyper flush.console pnorm sd terms var
Consider adding
  importFrom("stats", "dhyper", "pnorm", "sd", "terms", "var")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Note: found 10 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘forcats’
  All declared Imports should be used.
Note: found 4004 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
parse_counts: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘prettydoc’ ‘rmdformats’ ‘skimr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magick’ ‘tidyr’
  All declared Imports should be used.
File ‘CHsharp/libs/CHsharp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘stringr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘circlize’
  All declared Imports should be used.
cin: no visible global function definition for ‘pnorm’
gammaHRF: no visible global function definition for ‘dgamma’
intertest: no visible global function definition for ‘pnorm’
truncSum: no visible global function definition for ‘spline’
Undefined global functions or variables:
  dgamma pnorm spline
Consider adding
  importFrom("stats", "dgamma", "pnorm", "spline")
to your NAMESPACE file.
Package suggested but not available for checking: ‘userfriendlyscience’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RInside’ ‘circular’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
cit.assignBcmst: no visible binding for global variable ‘citbcmst’
cit.assignBcmst : <anonymous>: no visible global function definition
  for ‘median’
cit.assignBcmst: no visible global function definition for ‘prcomp’
cit.assignBcmst: no visible global function definition for ‘par’
cit.assignBcmst: no visible global function definition for ‘lines’
cit.assignBcmst: no visible global function definition for ‘legend’
cit.centroids : <anonymous>: no visible global function definition for
  ‘median’
cit.centroids : <anonymous>: no visible global function definition for
  ‘var’
cit.dist: no visible global function definition for ‘dist’
cit.dist: no visible global function definition for ‘as.dist’
cit.dist: no visible global function definition for ‘cor’
cit.distToCentroids: no visible global function definition for
  ‘quantile’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘median’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘mad’
Undefined global functions or variables:
  as.dist citbcmst cor dist legend lines mad median par prcomp quantile
  var
Consider adding
  importFrom("graphics", "legend", "lines", "par")
  importFrom("stats", "as.dist", "cor", "dist", "mad", "median",
             "prcomp", "quantile", "var")
to your NAMESPACE file.
cit.assignCcmst: no visible binding for global variable ‘citccmst’
cit.assignCcmst : <anonymous>: no visible global function definition
  for ‘median’
cit.assignCcmst : median.na: no visible global function definition for
  ‘median’
cit.assignCcmst: no visible global function definition for ‘prcomp’
cit.assignCcmst: no visible global function definition for ‘par’
cit.assignCcmst: no visible global function definition for ‘lines’
cit.assignCcmst: no visible global function definition for ‘legend’
cit.centroids : <anonymous>: no visible global function definition for
  ‘median’
cit.centroids : <anonymous>: no visible global function definition for
  ‘var’
cit.dist: no visible global function definition for ‘dist’
cit.dist: no visible global function definition for ‘as.dist’
cit.dist: no visible global function definition for ‘cor’
cit.distToCentroids: no visible global function definition for
  ‘quantile’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘median’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘mad’
Undefined global functions or variables:
  as.dist citccmst cor dist legend lines mad median par prcomp quantile
  var
Consider adding
  importFrom("graphics", "legend", "lines", "par")
  importFrom("stats", "as.dist", "cor", "dist", "mad", "median",
             "prcomp", "quantile", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
CityPlot: no visible global function definition for ‘read.table’
CityPlot: no visible global function definition for ‘tail’
CityPlot: no visible global function definition for ‘pdf’
CityPlot: no visible global function definition for ‘split.screen’
CityPlot: no visible global function definition for ‘screen’
CityPlot: no visible global function definition for ‘par’
CityPlot: no visible global function definition for ‘rect’
CityPlot: no visible global function definition for ‘text’
CityPlot: no visible global function definition for ‘lines’
CityPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off lines par pdf read.table rect screen split.screen tail text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "rect", "screen",
             "split.screen", "text")
  importFrom("utils", "read.table", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinyBS’
  All declared Imports should be used.
Note: found 29 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rggobi’
'library' or 'require' call to ‘rggobi’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
generate_data : <anonymous>: no visible global function definition for
  ‘runif’
knnf: no visible global function definition for ‘terms’
rescaler.default: no visible global function definition for ‘sd’
rescaler.default: no visible global function definition for ‘median’
rescaler.default: no visible global function definition for ‘mad’
simvar.numeric: no visible global function definition for ‘runif’
Undefined global functions or variables:
  mad median runif sd terms
Consider adding
  importFrom("stats", "mad", "median", "runif", "sd", "terms")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
Note: found 9 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Running examples in ‘clhs-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot.cLHS_result
> ### Title: Plot cLHS results
> ### Aliases: plot.cLHS_result
> 
> ### ** Examples
> 
> 
> df <- data.frame(
+   a = runif(1000), 
+   b = rnorm(1000), 
+   c = sample(LETTERS[1:5], size = 1000, replace = TRUE)
+ )
> 
> res <- clhs(df, size = 50, iter = 1000, use.cpp = FALSE, progress = FALSE, simple = FALSE)
Error in splitter_a(.data, .margins, .expand) : Invalid margin
Calls: clhs -> clhs.data.frame -> alply -> splitter_a
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘intro-clhs.Rmd’ using rmarkdown
Quitting from lines 125-127 (intro-clhs.Rmd) 
Error: processing vignette 'intro-clhs.Rmd' failed with diagnostics:
Invalid margin
--- failed re-building ‘intro-clhs.Rmd’

SUMMARY: processing the following file failed:
  ‘intro-clhs.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
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.
Package suggested but not available for checking: ‘scio’
clime: no visible global function definition for ‘cov’
cv.clime: no visible global function definition for ‘cov’
cv.clime: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  cov sd
Consider adding
  importFrom("stats", "cov", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
gxe.cc: no visible global function definition for ‘qnorm’
gxe.coh: no visible global function definition for ‘qnorm’
utility.cc: no visible global function definition for ‘qnorm’
utility.coh: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
Running ‘testthat.R’ [19s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(clinUtils)
  > 
  > test_check("clinUtils")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (2)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_palettes.R:32:7): An rrror is returned if the palette is not a function or a vector ──
  `getColorPalette(n = 1, palette = data.frame(A = 1))` did not throw an error.
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 300 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
socp: no visible global function definition for ‘as’
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Rd file 'socp.Rd':
  \usage lines wider than 90 characters:
     socp(A, b, c, kvec, type = rep('q',length(kvec)), use_sparse=TRUE, gamma_fac=.95, delta0 = .75, sigma0 = .25, mu0 = 0.01, zero_tol = 1e ... [TRUNCATED]

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
possible bashism in cleanup line 15 (brace expansion):
  rm -f src/*.{o,so,mod}
  possible bashism in cleanup line 17 (brace expansion):
  rm -f config.{log,status}
  possible bashism in cleanup line 22 (brace expansion):
  rm -f vignettes/*.{tex,aux,bbl,blg,log,toc,idx,ind,ilg,out,synctex.gz}
Found the following files/directories:
  ‘clusterhap_reports’
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.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘methods’ ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running examples in ‘clusterSim-Ex.R’ failed
The error most likely occurred in:

> ### Name: index.G1
> ### Title: Calculates Calinski-Harabasz pseudo F-statistic
> ### Aliases: index.G1
> ### Keywords: cluster
> 
> ### ** Examples
> 
> # Example 1
> library(clusterSim)
> data(data_ratio)
> c<- pam(data_ratio,10)
> index.G1(data_ratio,c$clustering)
Error in centers[i, ] <- x.k : incorrect number of subscripts on matrix
Calls: index.G1
Execution halted
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.
Namespaces in Imports field not imported from:
  ‘sp’ ‘spdep’
  All declared Imports should be used.
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.
Running examples in ‘ClusTorus-Ex.R’ failed
The error most likely occurred in:

> ### Name: kmeans.kspheres
> ### Title: K-Means Clustering to K-Spheres Clustering on Torus
> ### Aliases: kmeans.kspheres
> 
> ### ** Examples
> 
> data <- ILE[1:200, 1:2]
> 
> kmeans.kspheres(data, centers = 3, type = "general")
Error in data[, i] : subscript out of bounds
Calls: kmeans.kspheres ... kmeans.torus -> tor.minus -> cbind -> ang.minus -> on.torus
Execution halted
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Note: found 5626 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘datasets’ ‘dplyr’ ‘klaR’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
braycurtis: no visible global function definition for ‘as.dist’
czekanowski: no visible global function definition for ‘as.dist’
findComplementaryIndices: no visible global function definition for
  ‘na.omit’
genSimilarityProfile: no visible global function definition for ‘dist’
simprof: no visible global function definition for ‘dist’
simprof: no visible global function definition for ‘hclust’
simprof.plot : <local> : colorizer: no visible global function
  definition for ‘is.leaf’
simprof.plot: no visible global function definition for ‘rainbow’
simprof.plot: no visible global function definition for ‘dendrapply’
simprof.plot: no visible global function definition for ‘as.dendrogram’
Undefined global functions or variables:
  as.dendrogram as.dist dendrapply dist hclust is.leaf na.omit rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "as.dendrogram", "as.dist", "dendrapply", "dist",
             "hclust", "is.leaf", "na.omit")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
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.
cma_es: no visible global function definition for ‘rnorm’
f_rand: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
alpha.cronbach: no visible global function definition for ‘cov’
alpha.curve: no visible global function definition for ‘text’
Undefined global functions or variables:
  cov text
Consider adding
  importFrom("graphics", "text")
  importFrom("stats", "cov")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
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:
  ‘FNN’ ‘R.utils’ ‘SearchTrees’ ‘colorspace’ ‘colourpicker’
  ‘data.table’ ‘fields’ ‘mapproj’ ‘maps’ ‘maptools’ ‘ncdf4’ ‘raster’
  ‘rworldxtra’ ‘shinyFiles’ ‘shinyjs’ ‘shinythemes’ ‘sp’ ‘tcltk’ ‘xml2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘maptools’ ‘rgdal’ ‘rworldxtra’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘caret’ ‘e1071’ ‘epitools’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running examples in ‘cmstatr-Ex.R’ failed
The error most likely occurred in:

> ### Name: ad_ksample
> ### Title: Anderson-Darling K-Sample Test
> ### Aliases: ad_ksample
> 
> ### ** Examples
> 
> library(dplyr)

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

> 
> carbon.fabric %>%
+   filter(test == "WT") %>%
+   filter(condition == "RTD") %>%
+   ad_ksample(strength, batch)
Error: Argument `data` should be either a data.frame or NULL.
  Did you mean: `ad_ksample(x = .)` ?

Backtrace:
    █
 1. ├─`%>%`(...)
 2. └─cmstatr::ad_ksample(., strength, batch)
 3.   └─cmstatr:::verify_tidy_input(...)
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘adktest.Rmd’ using rmarkdown
--- finished re-building ‘adktest.Rmd’

--- re-building ‘cmstatr_Graphing.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 68-74 (cmstatr_Graphing.Rmd) 
Error: processing vignette 'cmstatr_Graphing.Rmd' failed with diagnostics:
Argument `data` should be either a data.frame or NULL.
  Did you mean: `basis_pooled_cv(x = .)` ?

--- failed re-building ‘cmstatr_Graphing.Rmd’

--- re-building ‘cmstatr_Tutorial.Rmd’ using rmarkdown
Quitting from lines 114-117 (cmstatr_Tutorial.Rmd) 
Error: processing vignette 'cmstatr_Tutorial.Rmd' failed with diagnostics:
Argument `data` should be either a data.frame or NULL.
  Did you mean: `anderson_darling_normal(x = .)` ?

--- failed re-building ‘cmstatr_Tutorial.Rmd’

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

Attaching package: 'testthat'

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

    is_null

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

    matches

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

    matches

Quitting from lines 207-216 (cmstatr_Validation.Rmd) 
Error: processing vignette 'cmstatr_Validation.Rmd' failed with diagnostics:
Argument `data` should be either a data.frame or NULL.
  Did you mean: `ad_ksample(x = .)` ?

--- failed re-building ‘cmstatr_Validation.Rmd’

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

SUMMARY: processing the following files failed:
  ‘cmstatr_Graphing.Rmd’ ‘cmstatr_Tutorial.Rmd’
  ‘cmstatr_Validation.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘htmltools’ ‘htmlwidgets’ ‘readxl’ ‘testthat’ ‘widgetframe’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
copynumberBootstrap: no visible global function definition for
  ‘txtProgressBar’
copynumberBootstrap: no visible global function definition for
  ‘quantile’
copynumberBootstrap: no visible global function definition for
  ‘setTxtProgressBar’
gethits: no visible global function definition for ‘read.table’
normalizeGC: no visible global function definition for ‘median’
plotCNOGpro: no visible global function definition for ‘par’
plotCNOGpro: no visible global function definition for ‘rainbow’
plotCNOGpro: no visible global function definition for ‘density’
plotCNOGpro: no visible global function definition for ‘polygon’
plotCNOGpro: no visible global function definition for ‘lines’
plotCNOGpro: no visible global function definition for ‘legend’
plotCNOGpro: no visible global function definition for ‘boxplot’
sampleChromosome: no visible global function definition for ‘median’
sampleChromosome: no visible binding for global variable ‘var’
setupEmissionMatrix: no visible global function definition for ‘dgeom’
store: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  boxplot density dgeom legend lines median par polygon quantile
  rainbow read.table setTxtProgressBar txtProgressBar var write.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "boxplot", "legend", "lines", "par", "polygon")
  importFrom("stats", "density", "dgeom", "median", "quantile", "var")
  importFrom("utils", "read.table", "setTxtProgressBar",
             "txtProgressBar", "write.table")
to your NAMESPACE file.
CNclusterNcenter: no visible global function definition for ‘median’
CNclusterNcenter: no visible binding for global variable ‘var’
breakIntoGaps: no visible global function definition for ‘runif’
centerprob: no visible global function definition for ‘pnorm’
getz: no visible global function definition for ‘predict’
smad: no visible global function definition for ‘mad’
smedian: no visible global function definition for ‘median’
smedian.sample: no visible global function definition for ‘median’
smedmad: no visible global function definition for ‘median’
smedmad: no visible global function definition for ‘mad’
Undefined global functions or variables:
  mad median pnorm predict runif var
Consider adding
  importFrom("stats", "mad", "median", "pnorm", "predict", "runif",
             "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
coalescentMCMC: no visible global function definition for
  ‘packageVersion’
coalescentMCMC : getparams: no visible global function definition for
  ‘nlminb’
sim.coalescent: no visible global function definition for ‘segments’
sim.coalescent: no visible global function definition for ‘points’
Undefined global functions or variables:
  nlminb packageVersion points segments
Consider adding
  importFrom("graphics", "points", "segments")
  importFrom("stats", "nlminb")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
Undocumented S4 methods:
  generic 'plot' and siglist 'cd.fit,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'library' or 'require' calls in package code:
  ‘lars’ ‘randomForest’ ‘ridge’ ‘snowfall’ ‘tree’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
COBRA : COBRA.lars: no visible global function definition for ‘lars’
COBRA : COBRA.lars: no visible global function definition for
  ‘predict.lars’
COBRA : COBRA.tree: no visible global function definition for ‘tree’
COBRA : COBRA.tree: no visible global function definition for
  ‘as.formula’
COBRA : COBRA.tree: no visible global function definition for ‘predict’
COBRA : COBRA.ridge: no visible global function definition for
  ‘linearRidge’
COBRA : COBRA.ridge: no visible global function definition for
  ‘as.formula’
COBRA : COBRA.ridge: no visible global function definition for
  ‘predict’
COBRA : COBRA.randomForest: no visible global function definition for
  ‘randomForest’
COBRA : COBRA.randomForest: no visible global function definition for
  ‘predict’
COBRA: no visible global function definition for ‘sfInit’
COBRA: no visible global function definition for ‘sfLibrary’
COBRA: no visible global function definition for ‘sfExportAll’
COBRA: no visible global function definition for ‘sfSapply’
COBRA: no visible global function definition for ‘sfStop’
COBRA: no visible global function definition for ‘write.table’
COBRA: no visible global function definition for ‘pdf’
COBRA: no visible global function definition for ‘points’
COBRA: no visible global function definition for ‘legend’
COBRA: no visible global function definition for ‘abline’
COBRA: no visible global function definition for ‘lines’
COBRA: no visible global function definition for ‘dev.off’
COBRA: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  abline as.formula dev.new dev.off lars legend linearRidge lines pdf
  points predict predict.lars randomForest sfExportAll sfInit sfLibrary
  sfSapply sfStop tree write.table
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("graphics", "abline", "legend", "lines", "points")
  importFrom("stats", "as.formula", "predict")
  importFrom("utils", "write.table")
to your NAMESPACE file.
File ‘COBRA/libs/COBRA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘nnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 14729 marked UTF-8 strings
Package which this enhances but not available for checking: ‘rkward’
Package which this enhances but not available for checking: ‘rkward’
Note: found 19 marked UTF-8 strings
Package in Depends field not imported from: ‘coda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
Package suggested but not available for checking: ‘userfriendlyscience’
Namespaces in Imports field not imported from:
  ‘graphics’ ‘jsonlite’ ‘rlang’ ‘tidyselect’ ‘vctrs’
  All declared Imports should be used.
Note: found 65 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 30244 marked UTF-8 strings
Found the following files/directories:
  ‘foo.R’ ‘foo.html’
Note: found 6 marked UTF-8 strings
Found the following files/directories:
  ‘fda7wnr6u.c’ ‘fda7wnr6u.o’ ‘fda7wnr6u.so’ ‘symbols.rds’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘methods’ ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
Malformed Description field: should contain one or more complete sentences.
Rd file 'fast.flexsim.Rd':
  \usage lines wider than 90 characters:
     fast.flexsim(scale = 2, island,dispersalscale = 51, allee = 1, T = 1000, initp,parcombination, spnum = 2, sourcetype = "constant", type ... [TRUNCATED]

Rd file 'flexsim.Rd':
  \usage lines wider than 90 characters:
     flexsim(scale = 2, dispersalscale = 51, allee = 1, T = 1000, prange, initp,spnum = 2, island=10, sourcetype = "constant", type, path =  ... [TRUNCATED]

Rd file 'make.heatmap.Rd':
  \usage lines wider than 90 characters:
     make.heatmap(mat, type = "gray", xname = "x", yname = "y", xlab = NULL, ylab = NULL, title = NULL)

Rd file 'sim.coarse.Rd':
  \usage lines wider than 90 characters:
     sim.coarse(island=10,scale = 2, dispersalscale = 51, allee = 1, T = 1000, prange, type, initp, path = NULL)

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘yaml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
BMDE: no visible global function definition for ‘quantile’
BMDU: no visible global function definition for ‘runif’
BMDU: no visible global function definition for ‘quantile’
FS: no visible global function definition for ‘qnorm’
GM: no visible global function definition for ‘qchisq’
QH: no visible global function definition for ‘qchisq’
SG : sgp: no visible global function definition for ‘ppois’
SG : sgp: no visible global function definition for ‘dpois’
WALD: no visible global function definition for ‘qchisq’
WALDCC: no visible global function definition for ‘qchisq’
WS: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  dpois ppois qchisq qnorm quantile runif
Consider adding
  importFrom("stats", "dpois", "ppois", "qchisq", "qnorm", "quantile",
             "runif")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘coin’ ‘ggplot2’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 4186 marked UTF-8 strings
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.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running examples in ‘colordistance-Ex.R’ failed
The error most likely occurred in:

> ### Name: convertColorSpace
> ### Title: Convert between color spaces
> ### Aliases: convertColorSpace
> 
> ### ** Examples
> 
> # Convert a single RGB triplet and then back convert it
> rgb_color <- c(0, 1, 0)
> lab_color <- colordistance::convertColorSpace(rgb_color,
+  from="sRGB", to="Lab", to.ref.white="D65")
From reference white:  
To reference white: D65
Subset of pixels for color conversion greater  than number of colors provided 
Converting all rows from sRGB color space to Lab color space
> rgb_again <- colordistance::convertColorSpace(lab_color,
+  from="Lab", to="sRGB", from.ref.white="D65")
From reference white: D65 
To reference white: 
Subset of pixels for color conversion greater  than number of colors provided 
Converting all rows from Lab color space to sRGB color space
Error in Lab[, 2L] : subscript out of bounds
Calls: <Anonymous> -> as.data.frame -> convertColor -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘binning-methods.Rmd’ using rmarkdown
Quitting from lines 63-68 (binning-methods.Rmd) 
Error: processing vignette 'binning-methods.Rmd' failed with diagnostics:
non-numeric argument to binary operator
--- failed re-building ‘binning-methods.Rmd’

--- re-building ‘color-metrics.Rmd’ using rmarkdown
--- finished re-building ‘color-metrics.Rmd’

--- re-building ‘color-spaces.Rmd’ using rmarkdown
Quitting from lines 107-131 (color-spaces.Rmd) 
Error: processing vignette 'color-spaces.Rmd' failed with diagnostics:
ncol(Lab) == 3L || length(Lab) == 3 is not TRUE
--- failed re-building ‘color-spaces.Rmd’

--- re-building ‘colordistance-introduction.Rmd’ using rmarkdown
Quitting from lines 154-156 (colordistance-introduction.Rmd) 
Error: processing vignette 'colordistance-introduction.Rmd' failed with diagnostics:
non-numeric argument to binary operator
--- failed re-building ‘colordistance-introduction.Rmd’

--- re-building ‘lab-analyses.Rmd’ using rmarkdown
Quitting from lines 66-70 (lab-analyses.Rmd) 
Error: processing vignette 'lab-analyses.Rmd' failed with diagnostics:
ncol(Lab) == 3L || length(Lab) == 3 is not TRUE
--- failed re-building ‘lab-analyses.Rmd’

SUMMARY: processing the following files failed:
  ‘binning-methods.Rmd’ ‘color-spaces.Rmd’
  ‘colordistance-introduction.Rmd’ ‘lab-analyses.Rmd’

Error: Vignette re-building failed.
Execution halted
cICA: no visible global function definition for ‘mvfft’
cICA: no visible global function definition for ‘ar.yw’
cICA: no visible global function definition for ‘rnorm’
scICA: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  ar.yw mvfft rnorm
Consider adding
  importFrom("stats", "ar.yw", "mvfft", "rnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Package in Depends field not imported from: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plotVenn2d : twoWayOverlap: no visible global function definition for
  ‘grid.polygon’
plotVenn2d : twoWayOverlap: no visible global function definition for
  ‘gpar’
plotVenn2d: no visible global function definition for ‘grid.text’
plotVenn2d: no visible global function definition for ‘gpar’
plotVenn2d: no visible global function definition for ‘grid.polygon’
plotVenn3d : twoWayOverlap: no visible global function definition for
  ‘grid.polygon’
plotVenn3d : twoWayOverlap: no visible global function definition for
  ‘gpar’
plotVenn3d: no visible global function definition for ‘grid.text’
plotVenn3d: no visible global function definition for ‘gpar’
plotVenn3d: no visible global function definition for ‘grid.polygon’
plotVenn4d : getCommonEllipse: no visible global function definition
  for ‘aggregate’
plotVenn4d : region.polygon: no visible global function definition for
  ‘head’
plotVenn4d : region.polygon: no visible global function definition for
  ‘grid.polygon’
plotVenn4d : region.polygon: no visible global function definition for
  ‘gpar’
plotVenn4d: no visible global function definition for ‘grid.text’
plotVenn4d: no visible global function definition for ‘gpar’
plotVenn4d: no visible global function definition for ‘pushViewport’
plotVenn4d: no visible global function definition for ‘viewport’
plotVenn4d: no visible global function definition for ‘grid.polygon’
plotVenn4d: no visible global function definition for ‘upViewport’
resizeCircles: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  aggregate gpar grid.polygon grid.text head pushViewport uniroot
  upViewport viewport
Consider adding
  importFrom("stats", "aggregate", "uniroot")
  importFrom("utils", "head")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 742 marked UTF-8 strings
generateMonochromaticColors: no visible global function definition for
  ‘col2rgb’
generateMonochromaticColors: no visible global function definition for
  ‘rgb’
generateMonochromaticColors: no visible global function definition for
  ‘tail’
hsv2rgb: no visible global function definition for ‘rgb’
rotational_dispersion: no visible global function definition for
  ‘col2rgb’
rotational_dispersion: no visible global function definition for
  ‘rgb2hsv’
tetradicColors: no visible global function definition for ‘head’
triadicColors: no visible global function definition for ‘head’
Undefined global functions or variables:
  col2rgb head rgb rgb2hsv tail
Consider adding
  importFrom("grDevices", "col2rgb", "rgb", "rgb2hsv")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
primary.colors: no visible global function definition for ‘rgb’
rgb.tables: no visible global function definition for ‘rgb’
ygobb: no visible global function definition for ‘approx’
ygobb: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  approx rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "approx")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘chi’ ‘dplyr’ ‘spatstat.utils’ ‘utils’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
competitive.test: no visible global function definition for ‘runif’
selfcontained.test : fun2: no visible global function definition for
  ‘qchisq’
selfcontained.test: no visible global function definition for ‘cov’
selfcontained.test: no visible global function definition for ‘qchisq’
selfcontained.test: no visible global function definition for ‘cor’
selfcontained.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cor cov pchisq qchisq runif
Consider adding
  importFrom("stats", "cor", "cov", "pchisq", "qchisq", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'library' or 'require' calls in package code:
  ‘lattice’ ‘rgl’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Rd file 'TMC.Rd':
  \usage lines wider than 90 characters:
     TMC(num.Iter = 50, data.Size = 100, make.Data = gen.Data, make.Params = gen.Params, model.List, weight.Vector = rep(1, times = length(m ... [TRUNCATED]
  \examples lines wider than 100 characters:
     result <- TMC(num.Iter = 3, model.List = make.Model.List.Reg(vars), msc.List = list(BIC, AIC, PRESS), var.Frame = vars)

Rd file 'make.Model.List.Reg.Rd':
  \usage lines wider than 90 characters:
     make.Model.List.Reg(fram, max.Size = min(8, dim(fram)[2]), no.Intercepts = FALSE, GLM = FALSE)

Rd file 'sarima.Sim.Rd':
  \usage lines wider than 90 characters:
     sarima.Sim(n = 20, period = 12, model, seasonal, rand.Gen.Fun = rnorm, rand.Gen.Seas = rnorm)

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘cometExactTest_plot.pdf’
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
CommT.anova: no visible global function definition for ‘aov’
CommT.legendpos: no visible global function definition for ‘quantile’
CommT.plotcolors: no visible global function definition for ‘hcl’
Undefined global functions or variables:
  aov hcl quantile
Consider adding
  importFrom("grDevices", "hcl")
  importFrom("stats", "aov", "quantile")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘GGally’ ‘RColorBrewer’ ‘abind’ ‘diagram’ ‘ggplot2’ ‘grid’ ‘gtable’
  ‘igraph’ ‘magrittr’ ‘plyr’ ‘purrr’ ‘reshape2’ ‘scales’ ‘useful’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
addxaxis: no visible global function definition for ‘par’
addxaxis: no visible global function definition for ‘axis’
addxaxis: no visible global function definition for ‘mtext’
eplot: no visible global function definition for ‘par’
eplot: no visible global function definition for ‘axis’
eplot: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  axis mtext par
Consider adding
  importFrom("graphics", "axis", "mtext", "par")
to your NAMESPACE file.
Package suggested but not available for checking: ‘CAM’
compareC: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
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.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘XML’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
compareODM: no visible global function definition for ‘xmlRoot’
compareODM: no visible global function definition for ‘xmlTreeParse’
compareODM: no visible global function definition for ‘xmlChildren’
compareODM: no visible global function definition for ‘xmlAttrs’
compareODM: no visible global function definition for ‘xmlValue’
Undefined global functions or variables:
  xmlAttrs xmlChildren xmlRoot xmlTreeParse xmlValue
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘numDeriv’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dcomplnorm: no visible global function definition for ‘grad’
dcomplnorm : f1: no visible global function definition for ‘dlnorm’
dcomplnorm : F1: no visible global function definition for ‘plnorm’
dcomplnorm : f1L: no visible global function definition for ‘dlnorm’
dcomplnorm : F1L: no visible global function definition for ‘plnorm’
pcomplnorm: no visible global function definition for ‘grad’
pcomplnorm : f1: no visible global function definition for ‘dlnorm’
pcomplnorm : F1: no visible global function definition for ‘plnorm’
pcomplnorm : F1L: no visible global function definition for ‘plnorm’
qcomplnorm: no visible global function definition for ‘grad’
qcomplnorm : f1: no visible global function definition for ‘dlnorm’
qcomplnorm : F1q: no visible global function definition for ‘qlnorm’
qcomplnorm : F1: no visible global function definition for ‘plnorm’
rcomplnorm: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dlnorm grad plnorm qlnorm runif
Consider adding
  importFrom("stats", "dlnorm", "plnorm", "qlnorm", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘hypergeo’ which was already attached by Depends.
  Please remove these calls from your code.
momentCompound: no visible global function definition for ‘integrate’
pgfIhypergeometric: no visible global function definition for ‘uniroot’
pgfIhyperpoisson: no visible global function definition for ‘uniroot’
pgfIkattitypeh1: no visible global function definition for ‘uniroot’
pgfIkattitypeh2: no visible global function definition for ‘uniroot’
pgfIneymantypeb: no visible global function definition for ‘uniroot’
pgfIneymantypec: no visible global function definition for ‘uniroot’
pgfIpoissonlindley: no visible global function definition for ‘uniroot’
pgfIthomas: no visible global function definition for ‘uniroot’
pgfIwaring: no visible global function definition for ‘uniroot’
pgfIyule: no visible global function definition for ‘uniroot’
rCompound: no visible global function definition for ‘runif’
Undefined global functions or variables:
  integrate runif uniroot
Consider adding
  importFrom("stats", "integrate", "runif", "uniroot")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
kef: no visible global function definition for ‘dgamma’
kef: no visible global function definition for ‘dlnorm’
simp_int: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dgamma dlnorm
Consider adding
  importFrom("stats", "approx", "dgamma", "dlnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
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.
Note: found 92 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [13s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(condformat)
  > 
  > test_check("condformat")
  == Failed tests ================================================================
  -- Failure (test-render-excel.R:8:3): condformat2excel generates a file --------
  nrow(openxlsx::read.xlsx(filename, 1)) not equal to `rows_to_write`.
  1/1 mismatches
  [1] 5 - 6 == -1
  -- Failure (test-render-excel.R:29:3): condformat2excel can write multiple sheets --
  nrow(openxlsx::read.xlsx(filename, 1)) not equal to `rows_to_write`.
  1/1 mismatches
  [1] 5 - 6 == -1
  -- Failure (test-render-excel.R:58:3): condformat2excel can overwrite a sheet without deleting others --
  openxlsx::read.xlsx(filename, "iris_head") not equal to `iris_head`.
  Names: 5 string mismatches
  Attributes: < Component "row.names": Numeric: lengths (5, 6) differ >
  Component 1: Numeric: lengths (5, 6) differ
  Component 2: Numeric: lengths (5, 6) differ
  Component 3: Numeric: lengths (5, 6) differ
  Component 4: Numeric: lengths (5, 6) differ
  Component 5: Lengths (5, 6) differ (string compare on first 5)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 64 ]
  Error: Test failures
  Execution halted
K1.norm: no visible global function definition for ‘dnorm’
K1.norm: no visible global function definition for ‘pnorm’
K1.t3: no visible global function definition for ‘pt’
K2.norm: no visible global function definition for ‘dnorm’
K2.norm: no visible global function definition for ‘pnorm’
K2.t3: no visible global function definition for ‘pt’
Undefined global functions or variables:
  dnorm pnorm pt
Consider adding
  importFrom("stats", "dnorm", "pnorm", "pt")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
Malformed Description field: should contain one or more complete sentences.
ml_solver: no visible global function definition for ‘approx’
select_kmax: no visible global function definition for ‘median’
Undefined global functions or variables:
  approx median
Consider adding
  importFrom("stats", "approx", "median")
to your NAMESPACE file.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [43s/42s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(condvis2)
  > 
  > test_check("condvis2")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-CVpredict.R:403:3): CVpredict kde ───────────────────────────────
  Error in `linbin(x, gpoints, truncate)`: 'list' object cannot be coerced to type 'double'
  Backtrace:
      █
   1. └─ks::kde(iris[, 1:2]) test-CVpredict.R:403:2
   2.   └─ks::hpi(...)
   3.     └─KernSmooth::dpik(x = x, level = nstage, gridsize = bgridsize)
   4.       └─KernSmooth:::linbin(x, gpoints, truncate)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 210 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Keras.Rmd’ using rmarkdown
--- finished re-building ‘Keras.Rmd’

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

--- re-building ‘mclust.Rmd’ using rmarkdown
Quitting from lines 177-179 (mclust.Rmd) 
Error: processing vignette 'mclust.Rmd' failed with diagnostics:
'list' object cannot be coerced to type 'double'
--- failed re-building ‘mclust.Rmd’

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

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

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘condvis-Ex.R’ failed
The error most likely occurred in:

> ### Name: arrangeC
> ### Title: Make a list of variable pairings for condition selecting plots
> ###   produced by plotxc
> ### Aliases: arrangeC
> 
> ### ** Examples
> 
> data(powerplant)
> 
> pairings <- arrangeC(powerplant)
> 
> dev.new(height = 2, width = 2 * length(pairings))
> par(mfrow = c(1, length(pairings)))
> 
> for (i in seq_along(pairings)){
+  plotxc(powerplant[, pairings[[i]]], powerplant[1, pairings[[i]]],
+    select.col = NA)
+ }
Error in hist.default(xc, xlab = name, ylab = "", main = "", cex.axis = cex.axis,  : 
  'x' must be numeric
Calls: plotxc -> hist -> hist.default
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running examples in ‘conf-Ex.R’ failed
The error most likely occurred in:

> ### Name: coversim
> ### Title: Confidence Region Coverage
> ### Aliases: coversim
> ### Keywords: distribution models univar
> 
> ### ** Examples
> 
> ## assess actual coverage at various alpha = {0.5, 0.1} given n = 30 samples,  completing
> ## 10 trials per parameterization (iter) for a normal(mean = 2, sd = 3) rv
> coversim(alpha = c(0.5, 0.1), "norm", n = 30, iter = 10, mu = 2, sigma = 3)
[1] "------------------ 30 samples in each of 10 iterations ---------------------"

[1] "...now using alpha: 0.5"

10% complete
20% complete
30% complete
40% complete
50% complete
60% complete
70% complete
80% complete
90% complete
100% complete
[1] "10 replications complete."
[1] "0 confidence regions contained the true parameters."
[1] "10 total errors."

[1] "...now using alpha: 0.1"

10% complete
20% complete
30% complete
40% complete
50% complete
60% complete
70% complete
80% complete
90% complete
100% complete
[1] "10 replications complete."
[1] "0 confidence regions contained the true parameters."
[1] "10 total errors."

[1] "coverage simulation summary (10 replications per parameterization):"
     alpha  n coverage errors
[1,]   0.5 30      NaN     10
[2,]   0.1 30      NaN     10
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'ylim' values
Calls: coversim -> plot -> plot.default -> localWindow -> plot.window
Execution halted
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
conicPlot: no visible global function definition for ‘palette’
conicPlotAsymptotes: no visible global function definition for
  ‘palette’
conicPlotAsymptotes: no visible global function definition for ‘abline’
conicPlotAxes: no visible global function definition for ‘palette’
conicPlotAxes: no visible global function definition for ‘abline’
plotDegenerateConic: no visible global function definition for ‘points’
plotDegenerateConic: no visible global function definition for ‘abline’
plotEllipsis: no visible global function definition for ‘lines’
plotEllipsis: no visible global function definition for ‘points’
plotHyperbola: no visible global function definition for ‘lines’
plotHyperbola: no visible global function definition for ‘points’
plotParabola: no visible global function definition for ‘lines’
Undefined global functions or variables:
  abline lines palette points
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "lines", "points")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'library' or 'require' call to ‘parallel’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘Rmpi’ ‘snow’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ConjointChecks: no visible global function definition for ‘makeCluster’
ConjointChecks: no visible global function definition for
  ‘clusterSetRNGStream’
ConjointChecks: no visible global function definition for
  ‘clusterApply’
ConjointChecks: no visible global function definition for ‘stopCluster’
omni.check: no visible global function definition for ‘runif’
omni.check: no visible global function definition for ‘quantile’
plot.checks: no visible global function definition for ‘mtext’
plot.checks: no visible global function definition for ‘text’
Undefined global functions or variables:
  clusterApply clusterSetRNGStream makeCluster mtext quantile runif
  stopCluster text
Consider adding
  importFrom("graphics", "mtext", "text")
  importFrom("stats", "quantile", "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘design_names.csv’ ‘design_numbers.csv’
  ‘encoded_orthogonal_factorial_design.csv’
  ‘orthogonal_factorial_design.csv’
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘RcppArmadillo’ ‘base’ ‘lwgeom’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Hmisc’ ‘dplyr’ ‘foreign’ ‘lavaan’ ‘openxlsx’ ‘purrr’ ‘semTools’
  ‘shinyWidgets’ ‘stringr’ ‘summarytools’ ‘waiter’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reshape’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘scales’ ‘sna’
  All declared Imports should be used.
Note: found 244 marked UTF-8 strings
File ‘ConsReg/libs/ConsReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GNU make is a SystemRequirements.
Running examples in ‘conText-Ex.R’ failed
The error most likely occurred in:

> ### Name: conText
> ### Title: Embedding regression
> ### Aliases: conText
> ### Keywords: conText
> 
> ### ** Examples
> 
> 
> library(quanteda)
Package version: 3.2.0
Unicode version: 12.1
ICU version: 65.1
Parallel computing: 24 of 24 threads used.
See https://quanteda.io for tutorials and examples.
> 
> # tokenize corpus
> toks <- tokens(cr_sample_corpus)
> 
> # build a tokenized corpus of contexts sorrounding a target term
> immig_toks <- tokens_context(x = toks, pattern = "immigr*", window = 6L)
1419 instances of "immigr*" found.
> 
> ## given the target word "immigration"
> set.seed(2021L)
> model1 <- conText(formula = immigration ~ party + gender,
+                  data = toks,
+                  pre_trained = cr_glove_subset,
+                  transform = TRUE, transform_matrix = cr_transform,
+                  bootstrap = TRUE, num_bootstraps = 10,
+                  stratify = TRUE,
+                  permute = TRUE, num_permutations = 100,
+                  window = 6, case_insensitive = TRUE,
+                  verbose = FALSE)
Error in fastDummies::dummy_cols(cov_vars, select_columns = non_indicator_vars,  : 
  select_columns is/are not in data. Please check data and spelling.
Calls: conText -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘quickstart.Rmd’ using rmarkdown
Package version: 3.2.0
Unicode version: 12.1
ICU version: 65.1
Parallel computing: 24 of 24 threads used.
See https://quanteda.io for tutorials and examples.

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

Creating a dfm from a tokens input...
 ...lowercasing
 ...found 400 documents, 4,836 features
 ...complete, elapsed time: 0.156 seconds.
Finished constructing a 400 x 4,836 sparse dfm.
Quitting from lines 312-325 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
select_columns is/are not in data. Please check data and spelling.
--- failed re-building ‘quickstart.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
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.
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Running examples in ‘control-Ex.R’ failed
The error most likely occurred in:

> ### Name: TF
> ### Title: Evaluate Transfer function Expressions
> ### Aliases: TF
> 
> ### ** Examples
> 
> 
> # Example taken from the GitHub page of Julia Control - an electric motor example
> J <- 2.0
> b <- 0.04
> K <- 1.0
> R <- 0.08
> L <- 1e-4
> P <- TF("K/(s*((J*s + b)*(L*s + R) + K^2))")
> Cls <- TF("P/(1 + P)") # closed-loop connection
Error in pracma::polymul(c(num2), c(den1)) : 
  Arguments 'p' and 'q' must be real or complex vectors.
Calls: TF -> eval -> eval -> / -> + -> <Anonymous>
Execution halted
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
maCooperative: no visible global function definition for ‘points’
maCooperative: no visible global function definition for ‘legend’
maPessimistic: no visible global function definition for ‘combn’
maRules: no visible global function definition for ‘capture.output’
mstCooperative: no visible global function definition for ‘points’
mstCooperative: no visible global function definition for ‘legend’
mstOptimistic: no visible global function definition for ‘combn’
mstPessimistic: no visible global function definition for ‘combn’
mstRules: no visible global function definition for ‘capture.output’
plotCoreSet: no visible global function definition for ‘points’
plotCoreSet: no visible global function definition for ‘polygon’
plotImputationSet: no visible global function definition for ‘par’
plotImputationSet: no visible global function definition for ‘box’
plotImputationSet: no visible global function definition for ‘polygon’
plotImputationSet: no visible global function definition for ‘text’
shapleyValue: no visible global function definition for ‘combn’
Undefined global functions or variables:
  box capture.output combn legend par points polygon text
Consider adding
  importFrom("graphics", "box", "legend", "par", "points", "polygon",
             "text")
  importFrom("utils", "capture.output", "combn")
to your NAMESPACE file.
Running examples in ‘cope-Ex.R’ failed
The error most likely occurred in:

> ### Name: cope
> ### Title: Coverage Probability Excursion (CoPE) Sets
> ### Aliases: cope cope-package
> 
> ### ** Examples
> 
> # An example using the ToySignal and the Toy Noise1 of this package.
> 
> # Set sample size.
> n = 30  
> # Generate n realizations of the toy noise field.
> Data = ToyNoise1(n = n)
> # Add the toy signal to the noise.
> Data$z = Data$z + rep(ToySignal()$z, n)
Error in t(x) - mean : non-numeric argument to binary operator
Calls: ToySignal -> single.peak -> matrix -> <Anonymous> -> backsolve
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cec2005benchmark’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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.
Error(s) in re-building vignettes:
--- re-building ‘coreheat-vignette.Rmd’ using rmarkdown
Quitting from lines 88-92 (coreheat-vignette.Rmd) 
Error: processing vignette 'coreheat-vignette.Rmd' failed with diagnostics:
SSL certificate problem: unable to get local issuer certificate
--- failed re-building ‘coreheat-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
advanceRNG: no visible global function definition for ‘runif’
randomEventMoves: no visible global function definition for ‘runif’
randomRescaledEventMoves: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
coreTDT_geneset: no visible global function definition for
  ‘write.table’
pvalue_calculator: no visible global function definition for ‘dbinom’
Undefined global functions or variables:
  dbinom write.table
Consider adding
  importFrom("stats", "dbinom")
  importFrom("utils", "write.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
compute.llh: no visible global function definition for ‘dnorm’
compute.u.hat.simple: no visible global function definition for ‘dnorm’
fit.CLM.1u.simple.start: no visible global function definition for
  ‘kmeans’
fit.CLMM.simple.start: no visible global function definition for
  ‘kmeans’
fit.CLMM.simple.start.NA: no visible global function definition for
  ‘kmeans’
Undefined global functions or variables:
  dnorm kmeans
Consider adding
  importFrom("stats", "dnorm", "kmeans")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘rmutil’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘rmarkdown’ ‘shinyWidgets’ ‘shinydashboard’
  ‘shinyjs’
  All declared Imports should be used.
Note: found 1187 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 578 marked UTF-8 strings
Note: found 438 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘profr’ ‘xtable’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked Latin-1 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Running examples in ‘correlation-Ex.R’ failed
The error most likely occurred in:

> ### Name: distance_mahalanobis
> ### Title: Mahalanobis distance and confidence interval (CI)
> ### Aliases: distance_mahalanobis
> 
> ### ** Examples
> 
> library(correlation)
> 
> distance_mahalanobis(iris[, 1:4])
Error in FUN(x, aperm(array(STATS, dims[perm]), order(perm)), ...) : 
  non-numeric argument to binary operator
Calls: distance_mahalanobis -> <Anonymous> -> sweep
Execution halted
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [34s/43s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(corrgram)
  > 
  > test_check("corrgram")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_misc.R:53:3): order argument ────────────────────────────────────
  Error in `ser_permutation_vector(order, method = method$name)`: 'list' object cannot be coerced to type 'integer'
  Backtrace:
      █
   1. └─corrgram::corrgram(mtcars, order = "GW") test_misc.R:53:2
   2.   ├─seriation::seriate(distx, method = order)
   3.   └─seriation:::seriate.dist(distx, method = order)
   4.     ├─seriation::ser_permutation(ser_permutation_vector(order, method = method$name))
   5.     └─seriation::ser_permutation_vector(order, method = method$name)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 19 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘corrplot-intro.Rmd’ using rmarkdown
Quitting from lines 188-211 (corrplot-intro.Rmd) 
Error: processing vignette 'corrplot-intro.Rmd' failed with diagnostics:
'list' object cannot be coerced to type 'integer'
--- failed re-building ‘corrplot-intro.Rmd’

SUMMARY: processing the following file failed:
  ‘corrplot-intro.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Running examples in ‘corrr-Ex.R’ failed
The error most likely occurred in:

> ### Name: rearrange
> ### Title: Re-arrange a correlation data frame
> ### Aliases: rearrange
> 
> ### ** Examples
> 
> x <- correlate(mtcars)

Correlation method: 'pearson'
Missing treated using: 'pairwise.complete.obs'

> 
> rearrange(x) # Default settings
# A tibble: 11 × 12
   term     mpg     vs    drat      am   gear    qsec    carb     hp     wt
   <chr>  <dbl>  <dbl>   <dbl>   <dbl>  <dbl>   <dbl>   <dbl>  <dbl>  <dbl>
 1 mpg   NA      0.664  0.681   0.600   0.480  0.419  -0.551  -0.776 -0.868
 2 vs     0.664 NA      0.440   0.168   0.206  0.745  -0.570  -0.723 -0.555
 3 drat   0.681  0.440 NA       0.713   0.700  0.0912 -0.0908 -0.449 -0.712
 4 am     0.600  0.168  0.713  NA       0.794 -0.230   0.0575 -0.243 -0.692
 5 gear   0.480  0.206  0.700   0.794  NA     -0.213   0.274  -0.126 -0.583
 6 qsec   0.419  0.745  0.0912 -0.230  -0.213 NA      -0.656  -0.708 -0.175
 7 carb  -0.551 -0.570 -0.0908  0.0575  0.274 -0.656  NA       0.750  0.428
 8 hp    -0.776 -0.723 -0.449  -0.243  -0.126 -0.708   0.750  NA      0.659
 9 wt    -0.868 -0.555 -0.712  -0.692  -0.583 -0.175   0.428   0.659 NA    
10 disp  -0.848 -0.710 -0.710  -0.591  -0.556 -0.434   0.395   0.791  0.888
11 cyl   -0.852 -0.811 -0.700  -0.523  -0.493 -0.591   0.527   0.832  0.782
# … with 2 more variables: disp <dbl>, cyl <dbl>
> rearrange(x, method = "HC")  # Different seriation method
Error in ser_permutation_vector(order, method = method$name) : 
  'list' object cannot be coerced to type 'integer'
Calls: rearrange ... seriate.dist -> ser_permutation -> ser_permutation_vector
Execution halted
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
corr.Qmatrix: no visible global function definition for ‘cor’
corr.Qmatrix: no visible global function definition for ‘cor.test’
summarise.Fst: no visible global function definition for ‘cor’
summarise.Fst: no visible global function definition for ‘sd’
summarise.lnPD: no visible global function definition for ‘sd’
Undefined global functions or variables:
  cor cor.test sd
Consider adding
  importFrom("stats", "cor", "cor.test", "sd")
to your NAMESPACE file.
Rd file 'corr.Qmatrix.Rd':
  \usage lines wider than 90 characters:
     corr.Qmatrix(filepath = "./", instruct = FALSE, rowncol = TRUE, avmax = TRUE, pvalue = FALSE, raw = TRUE, r = 0.99, p = 0.05)

Rd file 'rowncolMatrix-method.Rd':
  \examples lines wider than 100 characters:
     test <- rowncolMatrix(K = 3, filtermatrix = table(matrix(c("Y","Y","Y",NA,"Y","Y",NA,NA,"Y"),ncol = 3, byrow = TRUE)))

These lines will be truncated in the PDF manual.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
dist: no visible global function definition for ‘quantile’
edgecount: no visible global function definition for ‘reshape’
edgecutoff: no visible global function definition for ‘boxplot’
edgecutoff: no visible global function definition for ‘sd’
edgecutoff: no visible global function definition for ‘median’
edgecutoff: no visible global function definition for ‘IQR’
Undefined global functions or variables:
  IQR boxplot median quantile reshape sd
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "IQR", "median", "quantile", "reshape", "sd")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
GA_search : subset_score: no visible global function definition for
  ‘combn’
choose_lambda : subset_score: no visible global function definition for
  ‘combn’
cond.fyx: no visible global function definition for ‘var’
cond.fyx: no visible global function definition for ‘cor’
diff_gen_PPI: no visible global function definition for ‘cov’
diff_gen_PPI: no visible global function definition for ‘sd’
f.test: no visible binding for global variable ‘var’
get_quantiles : node_edge: no visible global function definition for
  ‘combn’
score_scaling: no visible global function definition for ‘hist’
score_scaling: no visible global function definition for ‘sd’
Undefined global functions or variables:
  combn cor cov hist sd var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "cor", "cov", "sd", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
Running examples in ‘cosinor2-Ex.R’ failed
The error most likely occurred in:

> ### Name: cosinor.PR
> ### Title: Percent Rhythm
> ### Aliases: cosinor.PR
> 
> ### ** Examples
> 
> fit.temperature<-cosinor.lm(Temperature~time(Time), period = 24, data = temperature_zg)
> cosinor.PR(fit.temperature)
          r Percent rhythm p-value
1 0.9838823      0.9680243       0
> 
> fit.november<-population.cosinor.lm(data = PANAS_november, time = PANAS_time,
+ period = 7)
Error in ((sdb^2) * (beta^2)) + (2 * covby * beta * gamma) : 
  non-conformable arrays
Calls: population.cosinor.lm
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘cosinor2.Rmd’ using rmarkdown
Loading required package: cosinor
Quitting from lines 47-48 (cosinor2.Rmd) 
Error: processing vignette 'cosinor2.Rmd' failed with diagnostics:
non-conformable arrays
--- failed re-building ‘cosinor2.Rmd’

SUMMARY: processing the following file failed:
  ‘cosinor2.Rmd’

Error: Vignette re-building failed.
Execution halted
cosinor.lm: no visible binding for global variable ‘na.omit’
cosinor.lm: no visible global function definition for ‘terms’
cosinor.lm: no visible global function definition for ‘as.formula’
cosinor.lm: no visible global function definition for ‘lm’
cosinor_analyzer: no visible binding for global variable ‘vitamind’
cosinor_analyzer : <anonymous>: no visible global function definition
  for ‘as.formula’
ggplot.cosinor.lm: no visible global function definition for ‘predict’
predict.cosinor.lm: no visible global function definition for ‘fitted’
predict.cosinor.lm: no visible global function definition for ‘predict’
simulate_cosinor: no visible global function definition for ‘runif’
simulate_cosinor: no visible global function definition for ‘rbinom’
simulate_cosinor: no visible global function definition for ‘rnorm’
summary.cosinor.lm: no visible global function definition for ‘vcov’
summary.cosinor.lm: no visible global function definition for ‘qnorm’
summary.cosinor.lm: no visible global function definition for ‘pnorm’
test_cosinor: no visible global function definition for ‘pchisq’
test_cosinor: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula fitted lm na.omit pchisq pnorm predict qnorm rbinom rnorm
  runif terms vcov vitamind
Consider adding
  importFrom("stats", "as.formula", "fitted", "lm", "na.omit", "pchisq",
             "pnorm", "predict", "qnorm", "rbinom", "rnorm", "runif",
             "terms", "vcov")
to your NAMESPACE file.