Package required but not available: ‘plotly’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xts', 'gstat', 'automap', 'maptools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rgdal', 'maptools', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'disordR', 'alabama', 'calibrator'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'rgdal'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'flowCore', 'rgeos'
Packages suggested but not available for checking: 'Bessel', 'jack'
Running examples in ‘HypergeoMat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BesselA
> ### Title: Type one Bessel function of Herz
> ### Aliases: BesselA
> 
> ### ** Examples
> 
> # for a scalar x, the relation with the Bessel J-function:
> t <- 2
> nu <- 3
> besselJ(t, nu)
[1] 0.1289432
> BesselA(m=15, t^2/4, nu) * (t/2)^nu
[1] 0.1289432
> # it also holds for a complex variable:
> t <- 1 + 2i
> Bessel::BesselJ(t, nu)
Error in loadNamespace(x) : there is no package called ‘Bessel’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [6s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(HypergeoMat)
  > 
  > test_check("HypergeoMat")
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 48 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-Bessel.R:6:3): Relation with Bessel-J for x scalar ──────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'Bessel'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-Bessel.R:6:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base withOneRestart(expr, restarts[[1L]])
   4.       └─base doWithOneRestart(return(expr), restart)
  ── Error (test-Jack.R:4:3): Schur expansion ────────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `library(jack)`: there is no package called 'jack'
  Backtrace:
      ▆
   1. └─base::library(jack) at test-Jack.R:4:2
  ── Error (test-Jack.R:52:3): Zonal expansion ───────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `library(jack)`: there is no package called 'jack'
  Backtrace:
      ▆
   1. └─base::library(jack) at test-Jack.R:52:2
  ── Error (test-Jack.R:100:3): ZonalQ expansion ─────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `library(jack)`: there is no package called 'jack'
  Backtrace:
      ▆
   1. └─base::library(jack) at test-Jack.R:100:2
  ── Error (test-Jack.R:148:3): MSF expansion ────────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `library(jack)`: there is no package called 'jack'
  Backtrace:
      ▆
   1. └─base::library(jack) at test-Jack.R:148:2
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 48 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/HyperG.Rcheck/00install.out’ for details.
Package required but not available: ‘matlib’

Package suggested but not available for checking: ‘webshot2’

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

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

Packages suggested but not available for checking:
  'R.matlab', 'devtools', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'raster', 'geometry', 'ks', 'rgeos', 'doParallel', 'caret'

Package suggested but not available for checking: ‘alphahull’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
conint: no visible global function definition for ‘sd’
findroot: no visible global function definition for ‘integrate’
hypothesis: no visible global function definition for ‘sd’
hypothesis: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate sd
Consider adding
  importFrom("stats", "integrate", "sd")
to your NAMESPACE file.
checkRd: (7) conint.Rd:29: invalid email address: (478996606@qq.com)
checkRd: (7) findroot.Rd:41: invalid email address: (478996606@qq.com)
checkRd: (7) hypothesis.Rd:66: invalid email address: (478996606@qq.com)
Rd file 'conint.Rd':
  \usage lines wider than 90 characters:
     conint(TrnX = NULL, TrnY = NULL, m, n1, n2, s1, s2, side = "both", alpha = 0.95, method = "n")

Rd file 'hypothesis-package.Rd':
  \examples lines wider than 100 characters:
     hypothesis(TrnX=c(3,4,5),TrnY=c(4,5,6),m,u0=4,3,3,s1=NULL,s2=NULL,sigma1=NULL,sigma2=NULL,alpha=0.05,method="n",H0="u=u0",p)

Rd file 'hypothesis.Rd':
  \usage lines wider than 90 characters:
     hypothesis(TrnX = NULL, TrnY = NULL, m, u0, n1, n2, s1 = NULL, s2 = NULL, sigma1 = NULL, sigma2 = NULL, alpha = 0.05, method = "n", H0  ... [TRUNCATED]
  \examples lines wider than 100 characters:
      hypothesis(TrnX=c(3,4,5),TrnY=c(4,5,6),m,u0=4,3,3,s1=NULL,s2=NULL,sigma1=NULL,sigma2=NULL,alpha=0.05,method="n",H0="u=u0",p)

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'stars', 'sjPlot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'orthopolynom', 'Rglpk'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hySpc.testthat.Rcheck/00install.out’ for details.
Packages required but not available: 'car', 'msm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hystReet.Rcheck/00install.out’ for details.
Package required but not available: ‘MCMCpack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'plotly', 'ComplexHeatmap', 'leaflet'
Running examples in ‘i2dash-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_component
> ### Title: Add content to an i2dashboard object.
> ### Aliases: add_component add_to_sidebar add_colormap add_link
> ###   add_component,i2dashboard,character-method
> ###   add_component,i2dashboard,function-method
> ###   add_component,i2dashboard,gg-method
> ###   add_component,i2dashboard,gt_tbl-method
> ###   add_component,i2dashboard,kableExtra-method
> ###   add_component,i2dashboard,Heatmap-method
> ###   add_component,i2dashboard,ANY-method add_link,i2dashboard-method
> ###   add_colormap,i2dashboard-method
> ###   add_to_sidebar,i2dashboard,character-method
> ###   add_to_sidebar,i2dashboard,function-method
> 
> ### ** Examples
> 
> library(magrittr)
> i2dashboard() -> dashboard
> myFunction <- function(dashboard) paste0("### Generate component\n\n",
+     "Lorem ipsum dolor sit amet\n")
> 
> dashboard %<>% add_component(component = myFunction)
> dashboard %<>% add_component(component = plotly::plot_ly(mtcars, x=~wt, y=~hp),
+     title = "Include htmlwidget")
Error in (function (cond)  : 
  error in evaluating the argument 'component' in selecting a method for function 'add_component': there is no package called ‘plotly’
Calls: %<>% ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘i2dash-extension.Rmd’ using rmarkdown
--- finished re-building ‘i2dash-extension.Rmd’

--- re-building ‘i2dash-intro.Rmd’ using rmarkdown

Attaching package: 'i2dash'

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

    title

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

    source

Quitting from lines 164-190 (i2dash-intro.Rmd) 
Error: processing vignette ‘i2dash-intro.Rmd’ failed with diagnostics:
there is no package called 'leaflet'
--- failed re-building ‘i2dash-intro.Rmd’

SUMMARY: processing the following file failed:
  ‘i2dash-intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘trending’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘FrF2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/iAdapt.Rcheck/00install.out’ for details.
Package required but not available: ‘dplR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'vcdExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘arfima’
Running examples in ‘iAR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: IARloglik
> ### Title: Maximum Likelihood Estimation of the IAR Model
> ### Aliases: IARloglik
> 
> ### ** Examples
> 
> #Generating IAR sample
> set.seed(6714)
> st<-gentime(n=100)
> y<-IARsample(phi=0.99,st=st,n=100)
> y<-y$series
> #Compute Phi
> phi=IARloglik(y=y,st=st)$phi
> print(phi)
[1] 0.9910354
> #Compute the standard deviation of innovations
> n=length(y)
> d=c(0,diff(st))
> phi1=phi**d
> yhat=phi1*as.vector(c(0,y[1:(n-1)]))
> plot(st,y,type='l')
> lines(st,yhat,col='red')
> sigma=var(y)
> nu=c(sigma,sigma*(1-phi1**(2))[-1])
> tau<-nu/sigma
> sigmahat<-mean(c((y-yhat)**2/tau))
> nuhat<-sigmahat*(1-phi1**(2))
> nuhat2<-sqrt(nuhat)
> #Equally spaced models
> require(arfima)
Loading required package: arfima
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘arfima’
> fit2<-arfima(y,order=c(1,0,0))
Error in arfima(y, order = c(1, 0, 0)) : could not find function "arfima"
Execution halted
Found the following files/directories:
  ‘AIC.txt’ ‘AICc.txt’ ‘IAS.pdf’ ‘IAS2.pdf’ ‘IAS3.pdf’
  ‘P.microlepis-AIC.txt’ ‘P.microlepis-AICc.txt’ ‘P.microlepis-IAS.pdf’
  ‘P.microlepis-IAS2.pdf’ ‘P.microlepis-IAS3.pdf’
Package required but not available: ‘qgraph’

Package suggested but not available for checking: ‘nparcomp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'tidyverse', 'caret', 'ggrepel', 'GGally', 'gutenbergr'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ibawds.Rcheck/00install.out’ for details.
Package required but not available: ‘lsa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
ibdhap.barplot: no visible global function definition for ‘rect’
ibdhap.compare.loci: no visible global function definition for ‘hist’
ibdhap.compare.segs: no visible global function definition for ‘tail’
ibdhap.make.calls: no visible global function definition for
  ‘count.fields’
ibdhap.make.calls: no visible global function definition for
  ‘read.table’
ibdhap.make.true: no visible global function definition for
  ‘read.table’
ibdhap.names: no visible global function definition for ‘count.fields’
ibdhap.names: no visible global function definition for ‘read.table’
ibdhap.reduce.states: no visible global function definition for
  ‘read.table’
ibdhap.reduce.states: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  count.fields hist read.table rect tail write.table
Consider adding
  importFrom("graphics", "hist", "rect")
  importFrom("utils", "count.fields", "read.table", "tail",
             "write.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'car', 'multcomp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Errors in running code in vignettes:
when running code in ‘ibdreg.Rnw’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘ibdreg.Rnw’... failed to complete the test
Packages required but not available: 'pedtools', 'ribd'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fields', 'rgeos', 'spdep'

Package suggested but not available for checking: ‘rgdal’

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
Packages required but not available: 'arules', 'rpart.plot'

Package suggested but not available for checking: ‘SparkR’

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

Package suggested but not available for checking: ‘ggfortify’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'betareg', 'lme4'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ibr.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/iBST.Rcheck/00install.out’ for details.
Package required but not available: ‘pamr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
ICA: 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
Packages required but not available:
  'Biostrings', 'BSgenome', 'GenomeInfoDb', 'GenomicRanges', 'IRanges'

Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm10'

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

Package suggested but not available for checking: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Packages required but not available:
  'caret', 'doParallel', 'plotROC', 'raster', 'leaflet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'KEGGgraph', 'mc2d'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rglpk’
Running ‘testthat.R’ [6s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("icarus")
  Loading required package: icarus
  [ FAIL 1 | WARN 18 | SKIP 0 | PASS 59 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_calibration_small_dataset.R:121:3): Calibration on minimum bounds checks out ──
  Error: Package Rglpk needed for this function to work. Please install it.
  Backtrace:
      ▆
   1. └─icarus::calibration(...) at test_calibration_small_dataset.R:121:2
   2.   └─icarus:::minBoundsCalib(...)
   3.     └─icarus:::solveMinBoundsCalib(...)
  
  [ FAIL 1 | WARN 18 | SKIP 0 | PASS 59 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ICBayes.Rcheck/00install.out’ for details.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fitdistrplus', 'icenReg', 'msm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘RLRsim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
'LazyData' is specified without a 'data' directory
Running examples in ‘ICCbin-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: iccbin
> ### Title: Estimates Intracluster Correlation coefficients (ICC) and it's
> ###   confidence intervals (CI)
> ### Aliases: iccbin
> 
> ### ** Examples
> 
> bccdata <- rcbin(prop = .4, prvar = .2, noc = 30, csize = 20, csvar = .2, rho = .2)
> iccbin(cid = cid, y = y, data = bccdata)
Warning in iccbin(cid = cid, y = y, data = bccdata) :
  One or Both of 'Zou and Donner's Modified Wald' Confidence Limits Fell Outside of [0, 1]
Error: Package 'lme4' is needed for methods 'lin' and 'sim'. Please install it.
Execution halted
Package required but not available: ‘glmmTMB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'partykit', 'icenReg', 'ipred'

Package suggested but not available for checking: ‘LTRCtrees’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
ICCbare: no visible global function definition for ‘na.omit’
ICCbare: no visible global function definition for ‘formula’
ICCbare: no visible global function definition for ‘replications’
ICCbare: no visible global function definition for ‘aggregate’
ICCbare: no visible global function definition for ‘anova’
ICCbare: no visible global function definition for ‘aov’
ICCbareF: no visible global function definition for ‘aggregate’
ICCest: no visible global function definition for ‘na.omit’
ICCest: no visible global function definition for ‘anova’
ICCest: no visible global function definition for ‘aov’
ICCest: no visible global function definition for ‘aggregate’
ICCest: no visible global function definition for ‘qf’
ICCest: no visible global function definition for ‘qnorm’
Nest: no visible global function definition for ‘qnorm’
effort : CIW: no visible global function definition for ‘qf’
effort: no visible global function definition for ‘axis’
effort: no visible global function definition for ‘lines’
effort: no visible global function definition for ‘legend’
Undefined global functions or variables:
  aggregate anova aov axis formula legend lines na.omit qf qnorm
  replications
Consider adding
  importFrom("graphics", "axis", "legend", "lines")
  importFrom("stats", "aggregate", "anova", "aov", "formula", "na.omit",
             "qf", "qnorm", "replications")
to your NAMESPACE file.
Package suggested but not available for checking: ‘icd’
Packages required but not available: 'graphite', 'metap', 'org.Hs.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ICEbox.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ICEinfer.Rcheck/00install.out’ for details.
Packages required but not available:
  'plotly', 'ggrepel', 'ggpubr', 'Hmisc', 'uwot', 'hdf5r'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/icenReg.Rcheck/00install.out’ for details.
Packages required but not available: 'Icens', 'smoothSurv'

Packages suggested but not available for checking:
  'interval', 'mixAK', 'bayesSurv', 'FHtest', 'glrt', 'icenReg',
  'frailtypack', 'MIICD', 'ICBayes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ICE.Rcheck/00install.out’ for details.
Packages required but not available: 'tidyverse', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'doParallel', 'leaflet', 'leafgl', 'leaflet.extras', 'leafsync'

Packages suggested but not available for checking:
  'mapview', 'plotly', 'CopernicusDEM'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ICGE.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ICGOR.Rcheck/00install.out’ for details.
Package required but not available: ‘xts’

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

Package suggested but not available for checking: ‘relaimpo’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'rugarch', 'xts', 'car', 'coefplot', 'fBasics', 'forecast', 'lmtest',
  'openair', 'papeR', 'timeSeries'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Depends: includes the non-default packages:
  'lattice', 'caTools', 'gdata', 'gtools', 'gplots', 'parallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/iCluster.Rcheck/00install.out’ for details.
Package required but not available: ‘EbayesThresh’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ICODS.Rcheck/00install.out’ for details.
Package required but not available: ‘rgdal’

Package suggested but not available for checking: ‘dendextend’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rgdal', 'raster'
Error(s) in re-building vignettes:
  ...
--- re-building ‘icosa.Rmd’ using rmarkdown
Quitting from lines 13-20 (icosa.Rmd) 
Error: processing vignette ‘icosa.Rmd’ failed with diagnostics:
there is no package called 'rgdal'
--- failed re-building ‘icosa.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘multcomp’

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

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

Package suggested but not available for checking: ‘REPPlab’

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

Package suggested but not available for checking: ‘ICSNP’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ICS', 'ICSOutlier', 'ICSNP', 'rrcov'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
PH.ICsurv.EM: no visible global function definition for ‘quantile’
PH.ICsurv.EM: no visible global function definition for ‘optim’
fast.PH.ICsurv.EM: no visible global function definition for ‘quantile’
fast.PH.ICsurv.EM: no visible global function definition for ‘optim’
Undefined global functions or variables:
  optim quantile
Consider adding
  importFrom("stats", "optim", "quantile")
to your NAMESPACE file.
Packages required but not available:
  'ICS', 'ICSNP', 'survey', 'GGally', 'xts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘metR’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Using_ICvectorfields.Rmd’ using rmarkdown
Quitting from lines 19-25 (Using_ICvectorfields.Rmd) 
Error: processing vignette ‘Using_ICvectorfields.Rmd’ failed with diagnostics:
there is no package called 'metR'
--- failed re-building ‘Using_ICvectorfields.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'FD', 'picante', 'spatstat', 'spatstat.geom', 'spatstat.core',
  'spatstat.random'

Packages suggested but not available for checking: 'ecespa', 'vegan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

idbg.interact: no visible global function definition for
  ‘capture.output’
idbg.interact: no visible global function definition for ‘timestamp’
idbg.print_breakpoints: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output timestamp
Consider adding
  importFrom("utils", "capture.output", "timestamp")
to your NAMESPACE file.
Package suggested but not available for checking: ‘plotly’
Package suggested but not available for checking: ‘readr’
Package required but not available: ‘tmvtnorm’

Package suggested but not available for checking: ‘RSGHB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'sqldf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rggobi', 'DendSer'
Packages required but not available: 'spacetime', 'FRK'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ismev’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggpubr', 'phytools'
Package required but not available: ‘lme4’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'viridis', 'furrr'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IDPSurvival.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
comp.uri: no visible global function definition for ‘quantile’
est.IDR: no visible global function definition for ‘ecdf’
get.pseudo.mix: no visible global function definition for ‘pnorm’
get.uri.2d: no visible global function definition for ‘smooth.spline’
get.uri.2d: no visible global function definition for ‘predict’
Undefined global functions or variables:
  ecdf pnorm predict quantile smooth.spline
Consider adding
  importFrom("stats", "ecdf", "pnorm", "predict", "quantile",
             "smooth.spline")
to your NAMESPACE file.
Package required but not available: ‘doSNOW’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'IDSL.IPA', 'doSNOW', 'GA', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'IDSL.IPA', 'IDSL.UFA', 'doSNOW'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'doParallel', 'spatstat.core', 'spatstat.geom'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'spatstat', 'rgdal', 'maptools'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Southeast-US-Engineering-Weather-Map.Rmd’ using rmarkdown
Quitting from lines 21-110 (Southeast-US-Engineering-Weather-Map.Rmd) 
Error: processing vignette ‘Southeast-US-Engineering-Weather-Map.Rmd’ failed with diagnostics:
package rgdal is required for spTransform methods
--- failed re-building ‘Southeast-US-Engineering-Weather-Map.Rmd’

--- re-building ‘US-Engineering-Weather-Map.Rmd’ using rmarkdown
Quitting from lines 21-106 (US-Engineering-Weather-Map.Rmd) 
Error: processing vignette ‘US-Engineering-Weather-Map.Rmd’ failed with diagnostics:
package rgdal is required for spTransform methods
--- failed re-building ‘US-Engineering-Weather-Map.Rmd’

SUMMARY: processing the following files failed:
  ‘Southeast-US-Engineering-Weather-Map.Rmd’
  ‘US-Engineering-Weather-Map.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'gWidgets2', 'gWidgets2tcltk', 'reader'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'iemisc', 'ie2misc', 'qdap'
Packages required but not available: 'gsubfn', 'rgdal'

Package suggested but not available for checking: ‘ie2misc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tm’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Analysis-using-tm-vignette.Rmd’ using rmarkdown
Quitting from lines 20-122 (Analysis-using-tm-vignette.Rmd) 
Error: processing vignette ‘Analysis-using-tm-vignette.Rmd’ failed with diagnostics:
could not find function "DocumentTermMatrix"
--- failed re-building ‘Analysis-using-tm-vignette.Rmd’

--- re-building ‘View-PDFs-vignette.Rmd’ using rmarkdown
--- finished re-building ‘View-PDFs-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘Analysis-using-tm-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'qlcMatrix', 'expm', 'HDCI', 'doParallel', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/iFad.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

ifa.em: no visible global function definition for ‘runif’
ifa.init.pca: no visible global function definition for ‘var’
ifa.init.pca: no visible global function definition for ‘cor’
ifa.init.pca: no visible global function definition for ‘runif’
ifa.init.random: no visible global function definition for ‘runif’
ifa.init.random: no visible global function definition for ‘var’
Undefined global functions or variables:
  cor runif var
Consider adding
  importFrom("stats", "cor", "runif", "var")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ifaTools.Rcheck/00install.out’ for details.
Package required but not available: ‘latticeExtra’

Package suggested but not available for checking: ‘IFCdata’

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

Packages suggested but not available for checking:
  'forecast', 'timeSeries', 'timetk'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/iGasso.Rcheck/00install.out’ for details.
Packages required but not available: 'ggpubr', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rio', 'haven', 'readODS', 'Hmisc', 'ggformula', 'mapsf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'laGP', 'tgp'
Running examples in ‘IGP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: IGP_LOOEC_laGP_GauPro
> ### Title: IGP R6 object for fitting laGP_GauPro model with leave-one-out
> ###   error correction
> ### Aliases: IGP_LOOEC_laGP_GauPro
> 
> ### ** Examples
> 
> n <- 40
> d <- 2
> n2 <- 20
> f1 <- function(x) {sin(2*pi*x[1]) + sin(2*pi*x[2])}
> X1 <- matrix(runif(n*d),n,d)
> Z1 <- apply(X1,1,f1) + rnorm(n, 0, 1e-3)
> X2 <- matrix(runif(n2*d),n2,d)
> Z2 <- apply(X2,1,f1)
> XX1 <- matrix(runif(10),5,2)
> ZZ1 <- apply(XX1, 1, f1)
> u <- IGP_LOOEC_laGP_GauPro$new(X=X1,Z=Z1)
Error in loadNamespace(x) : there is no package called ‘laGP’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(IGP)
  > 
  > test_check("IGP")
  [1] "laGP"
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_IGP.R:11:5): 1D data works ──────────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'laGP'
  Backtrace:
      ▆
   1. ├─IGP::IGP(package = package, X = X1, Z = Z1) at test_IGP.R:11:4
   2. │ └─IGP_laGP$new(X = X, Z = Z, ...)
   3. │   └─IGP initialize(...)
   4. │     └─self$init(...)
   5. │       └─self$.init(...)
   6. └─base::loadNamespace(x)
   7.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   8.     └─base withOneRestart(expr, restarts[[1L]])
   9.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘irlba’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘graph’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/igraphtosonia.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘metR’
Error(s) in re-building vignettes:
  ...
--- re-building ‘igrf.Rmd’ using rmarkdown
Quitting from lines 55-85 (igrf.Rmd) 
Error: processing vignette ‘igrf.Rmd’ failed with diagnostics:
there is no package called 'metR'
--- failed re-building ‘igrf.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'factoextra', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘R2jags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'strex'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'multcomp', 'fda.usc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘raster’
Packages required but not available: 'dae', 'Hmisc', 'GGally'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'raster', 'spatstat.geom'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/imager.Rcheck/00install.out’ for details.
Package required but not available: ‘doParallel’

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/imageviewer.Rcheck/00install.out’ for details.
Package required but not available: ‘imager’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘C50’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'SingleCellExperiment', 'SummarizedExperiment', 'S4Vectors',
  'spatstat.geom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'devtools', 'readr', 'Hmisc', 'readODS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'IsingSampler', 'qgraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'MBESS'

Package suggested but not available for checking: ‘mediation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rfast’

Packages suggested but not available for checking: 'mcclust', 'Rmpfr'

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

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

Packages suggested but not available for checking:
  'caret', 'future.callr', 'glmnet', 'mlr', 'mlr3', 'party', 'partykit'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'clusterProfiler', 'GSEABase', 'corrr', 'GSVA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'CDM', 'sirt', 'TAM'

Package which this enhances but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'factoextra', 'fpc', 'ggrepel', 'airr', 'ggalluvial', 'ggpubr',
  'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Biostrings', 'repmis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'missForest', 'missMDA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lvmisc', 'vroom'

Package suggested but not available for checking: ‘accdata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'odbc', 'RJDBC'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/implyr.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ImportanceIndice.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Hmisc', 'haven'

Package suggested but not available for checking: ‘compareGroups’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'haven', 'rgdal'

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
Skipping vignette re-building
Packages suggested but not available for checking: 'R.rsp', 'xts'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Running ‘testthat.R’ [46s/70s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(imputeFin)
  > 
  > test_check("imputeFin")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 97 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-condMeanCov.R:4:1): (code run outside of `test_that()`) ─────────
  <packageNotFoundError/error/condition>
  Error in `library(xts)`: there is no package called 'xts'
  Backtrace:
      ▆
   1. └─base::library(xts) at test-condMeanCov.R:4:0
  ── Error (test-misc.R:14:3): is_inner_NA() works ───────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'xts'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-misc.R:14:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base withOneRestart(expr, restarts[[1L]])
   4.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 97 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'tmvtnorm', 'pcaMethods'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
impute.mdr: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Rd file 'impute.mdr.Rd':
  \usage lines wider than 90 characters:
     impute.mdr(dataset, colresp, cs, combi, cv.fold = 10, na.method = 0, max_iter = 30, randomize = FALSE)

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Packages required but not available:
  'gamlss', 'extremevalues', 'gamlss.dist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'caret', 'glmnet', 'Cubist', 'mboost', 'earth'
Packages required but not available: 'forecast', 'imputeTS'

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

Packages suggested but not available for checking:
  'R.rsp', 'timeSeries', 'xts'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ltm', 'lme4'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘survey’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/inca.Rcheck/00install.out’ for details.
Packages required but not available:
  'siggenes', 'multtest', 'genefilter', 'RankProd'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'dtw', 'dtwclust', 'R.rsp', 'dendextend'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
GNU make is a SystemRequirements.
Packages required but not available: 'maptools', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tmvtnorm', 'doParallel'

Package suggested but not available for checking: ‘survey’

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

Package suggested but not available for checking: ‘future.callr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IndepTest.Rcheck/00install.out’ for details.
Packages required but not available: 'fGarch', 'xts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rgeos’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/indicspecies.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'viridis', 'DoE.base', 'car', 'ggforce', 'ggraph', 'agricolae',
  'RcmdrMisc'
Packages required but not available: 'hdi', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
IDM.bootCI: no visible global function definition for ‘cov’
IDM.bootCI: no visible global function definition for ‘cor’
IDM.bootCI: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  cor cov quantile
Consider adding
  importFrom("stats", "cor", "cov", "quantile")
to your NAMESPACE file.
Rd file 'IDM.bootCI.Rd':
  \examples lines wider than 100 characters:
     #a built-in dataset fish is used. This data gives sizes of 53 female stickleback measured at the age of 17, 45, 80, and 115 days.
     #figure showing first two trajectories and percentages of variations accounted for by each trajectory.
     barplot(out$Percent.trajectory,ylim=c(0,105),las=1,names.arg=c("1","2","3","4"), ylab="Percentage of variation",cex.lab=1.35,cex.axis=1 ... [TRUNCATED]
     plot(age,out$Trajectories97.5CI[,1],type="l",lty=2,ylim=c(-1,1),las=1,ylab="Trajectory value",xlab="Age (days)",cex.lab=1.35,cex.axis=1 ... [TRUNCATED]
     plot(age,out$Trajectories97.5CI[,2],type="l",lty=2,ylim=c(-1,1),las=1,ylab="Trajectory value",xlab="Age (days)",cex.lab=1.35,cex.axis=1 ... [TRUNCATED]

Rd file 'p.function.Rd':
  \examples lines wider than 100 characters:
     temp2b=(-1)^i*factorial(j)/(factorial(i)*factorial(j-i))*factorial(2*j-2*i)/(factorial(j)*factorial(2*j-2*i-j))*x^(j-2*i)

These lines will be truncated in the PDF manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/InferenceSMR.Rcheck/00install.out’ for details.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Error(s) in re-building vignettes:
  ...
--- re-building ‘anova.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 17-20 (anova.Rmd) 
Error: processing vignette ‘anova.Rmd’ failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘anova.Rmd’

--- re-building ‘chi_squared.Rmd’ using rmarkdown
Quitting from lines 17-20 (chi_squared.Rmd) 
Error: processing vignette ‘chi_squared.Rmd’ failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘chi_squared.Rmd’

--- re-building ‘infer.Rmd’ using rmarkdown
Quitting from lines 34-36 (infer.Rmd) 
Error: processing vignette ‘infer.Rmd’ failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘infer.Rmd’

--- re-building ‘observed_stat_examples.Rmd’ using rmarkdown
Quitting from lines 27-29 (observed_stat_examples.Rmd) 
Error: processing vignette ‘observed_stat_examples.Rmd’ failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘observed_stat_examples.Rmd’

--- re-building ‘t_test.Rmd’ using rmarkdown
Quitting from lines 17-20 (t_test.Rmd) 
Error: processing vignette ‘t_test.Rmd’ failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘t_test.Rmd’

SUMMARY: processing the following files failed:
  ‘anova.Rmd’ ‘chi_squared.Rmd’ ‘infer.Rmd’
  ‘observed_stat_examples.Rmd’ ‘t_test.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/infinitefactor.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/InfiniumPurify.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'xlsx', 'GGally'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/influence.SEM.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'Hmisc', 'NNS'
Packages required but not available: 'bit64', 'nanotime'

Package suggested but not available for checking: ‘httptest’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
BugReports field should be the URL of a single webpage
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/InformativeCensoring.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘gurobi’
Package required but not available: ‘relevent’

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

Package suggested but not available for checking: ‘rNOMADS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
getInfra: no visible global function definition for ‘txtProgressBar’
getInfra: no visible global function definition for ‘download.file’
getInfra: no visible global function definition for ‘setTxtProgressBar’
getInfra : <anonymous>: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "download.file", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘bingFileContents.txt’ ‘japanInfraBing.png’
Packages required but not available: 'spaMM', 'blackbox', 'viridis'

Package suggested but not available for checking: ‘Rmixmod’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘spdep’

Package suggested but not available for checking: ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rgdal', 'rgeos'

Packages suggested but not available for checking:
  'ggmap', 'ggpolypath', 'INLA', 'maptools', 'raster', 'sn',
  'spatstat.geom', 'spatstat.core', 'spatstat', 'sphereplot'

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

Packages suggested but not available for checking:
  'dataRetrieval', 'inlmisc', 'maptools', 'rgdal', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘future.apply’
Packages required but not available:
  'GA', 'leaflet', 'raster', 'rgdal', 'rgeos'

Packages suggested but not available for checking:
  'alphahull', 'doParallel', 'doRNG', 'gstat', 'maptools'

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

Package suggested but not available for checking: ‘inlmisc’

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

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'wordcloud', 'tm', 'entropart', 'metacom', 'R.devices'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ExPosition’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘readr’
Running examples in ‘INQC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: climdex2ecad
> ### Title: Converter from the ClimDex format into the ECA&D format (blended
> ###   version)
> ### Aliases: climdex2ecad
> 
> ### ** Examples
> 
> #Set a temporal working directory:
> wd <- tempdir(); wd0 <- setwd(wd)
> #Create subdirectory where raw data files in the ClimDex format have to be located
> dir.create(file.path(wd, "raw_ClimDex"))
> #Extract the ClimDex data and station files from the example data folder
> path2stalist<-system.file("extdata", "stations.csv", package = "INQC")
> stalist<-readr::read_lines_raw(path2stalist)
Error in loadNamespace(x) : there is no package called ‘readr’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'ggbeeswarm', 'ggpubr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyverse’
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(insee)
  > 
  > test_check("insee")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_all.R:4:1): (code run outside of `test_that()`) ─────────────────
  <packageNotFoundError/error/condition>
  Error in `library(tidyverse)`: there is no package called 'tidyverse'
  Backtrace:
      ▆
   1. └─base::library(tidyverse) at test_all.R:4:0
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘devtools’
Error(s) in re-building vignettes:
  ...
--- re-building ‘insiderTrades.Rmd’ using rmarkdown
Quitting from lines 17-18 (insiderTrades.Rmd) 
Error: processing vignette ‘insiderTrades.Rmd’ failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘insiderTrades.Rmd’

--- re-building ‘pullAndScrape.Rmd’ using rmarkdown
Quitting from lines 17-18 (pullAndScrape.Rmd) 
Error: processing vignette ‘pullAndScrape.Rmd’ failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘pullAndScrape.Rmd’

SUMMARY: processing the following files failed:
  ‘insiderTrades.Rmd’ ‘pullAndScrape.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'AER', 'afex', 'BayesFactor', 'betareg', 'biglm', 'blavaan', 'blme',
  'brms', 'censReg', 'cgam', 'coxme', 'cplm', 'epiR', 'feisr',
  'fungible', 'gam', 'gamlss', 'gamm4', 'glmmTMB', 'gmnl', 'ivreg',
  'JM', 'lfe', 'lme4', 'lmtest', 'MCMCglmm', 'merTools', 'metaBMA',
  'mlogit', 'multgee', 'panelr', 'plm', 'quantreg', 'rms', 'robustlmm',
  'rstanarm', 'speedglm', 'survey', 'truncreg'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/InSilicoVA.Rcheck/00install.out’ for details.
Package required but not available: ‘raster’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'R.utils'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/instaR.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Packages required but not available:
  'ciTools', 'DHARMa', 'evtree', 'fitdistrplus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'gstat', 'automap', 'doParallel', 'rgdal'

Package which this enhances but not available for checking: ‘psgp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'alabama', 'doParallel'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ltm', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Biobase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘Error_Estimation_Response_1.tiff’ ‘Error_Estimation_Response_2.tiff’
  ‘Error_Estimation_Response_3.tiff’
Package required but not available: ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rgdal', 'diffeR', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'sna', 'spatstat.geom', 'spdep', 'viridis'

Package suggested but not available for checking: ‘spatstat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'GenomicRanges', 'GenomeInfoDb', 'IRanges', 'GenomicAlignments',
  'biomaRt', 'Rsamtools', 'DESeq2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'msm', 'rms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'msm', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'lme4', 'survey'

Packages which this enhances but not available for checking:
  'brms', 'rstanarm'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/InteractiveIGraph.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
interact: no visible global function definition for ‘cor’
standardize.matrix: no visible binding for global variable ‘var’
standardize.matrix: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  cor sd var
Consider adding
  importFrom("stats", "cor", "sd", "var")
to your NAMESPACE file.
Package suggested but not available for checking: ‘doParallel’
Package required but not available: ‘xlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/interferenceCI.Rcheck/00install.out’ for details.
Packages required but not available: 'doParallel', 'lfe', 'lmtest', 'AER'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/interimApp.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/interlineaR.Rcheck/00install.out’ for details.
Package required but not available: ‘arm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  s_hull_pro.cpp:1639:9: warning: ‘tx.Triad::ro’ is used uninitialized [-Wuninitialized]
  s_hull_pro.cpp:1639:9: warning: ‘tx.Triad::R’ is used uninitialized [-Wuninitialized]
  s_hull_pro.cpp:1639:13: warning: ‘tx2.Triad::ro’ is used uninitialized [-Wuninitialized]
  s_hull_pro.cpp:1639:13: warning: ‘tx2.Triad::R’ is used uninitialized [-Wuninitialized]
  s_hull_pro.cpp:781:9: warning: ‘tx.Triad::ro’ is used uninitialized [-Wuninitialized]
  s_hull_pro.cpp:781:9: warning: ‘tx.Triad::R’ is used uninitialized [-Wuninitialized]
  s_hull_pro.cpp:781:13: warning: ‘tx2.Triad::ro’ is used uninitialized [-Wuninitialized]
  s_hull_pro.cpp:781:13: warning: ‘tx2.Triad::R’ is used uninitialized [-Wuninitialized]
  s_hull_pro.cpp:1188:13: warning: ‘tx2.Triad::ro’ is used uninitialized [-Wuninitialized]
  s_hull_pro.cpp:1188:13: warning: ‘tx2.Triad::R’ is used uninitialized [-Wuninitialized]
  s_hull_pro.cpp:1188:9: warning: ‘tx.Triad::ro’ is used uninitialized [-Wuninitialized]
  s_hull_pro.cpp:1188:9: warning: ‘tx.Triad::R’ is used uninitialized [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/interp.Rcheck/00install.out’ for details.
Package required but not available: ‘ggbeeswarm’

Package suggested but not available for checking: ‘PairedData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rdisop', 'doParallel', 'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/interpretR.Rcheck/00install.out’ for details.
Package required but not available: ‘NMF’

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

Package suggested but not available for checking: ‘lmtest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/intervalaverage.Rcheck/00install.out’ for details.
Package required but not available: ‘Icens’

Package suggested but not available for checking: ‘coin’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
interventionEffects: no visible binding for global variable ‘sd’
interventionEffects: no visible global function definition for ‘pt’
interventionEffects: no visible global function definition for ‘sd’
interventionalInference: no visible global function definition for ‘sd’
interventionalInferenceAdvanced: no visible global function definition
  for ‘sd’
linesROC: no visible global function definition for ‘segments’
plotMaxML: no visible global function definition for ‘segments’
Undefined global functions or variables:
  pt sd segments
Consider adding
  importFrom("graphics", "segments")
  importFrom("stats", "pt", "sd")
to your NAMESPACE file.
Packages required but not available: 'clinUtils', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'agricolae', 'FactoMineR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gstat', 'raster'

Packages suggested but not available for checking:
  'doParallel', 'latticeExtra'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'NMF', 'InterSIM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/intrinsicDimension.Rcheck/00install.out’ for details.
Package required but not available: ‘MCMCpack’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'msm', 'tmvtnorm', 'MHadaptive'

Package suggested but not available for checking: ‘smoothmest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Hmisc', 'memisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package vignette with placeholder title ‘Vignette Title’:
  ‘intubate.Rmd’
Packages required but not available: 'earth', 'lmtest', 'quantreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'mboost'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/InvasionCorrection.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plotly’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘sparseLRMatrix’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/invGauss.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘iNZightPlots’
Packages required but not available: 'iNZightTools', 'quantreg', 'survey'

Packages suggested but not available for checking:
  'ggbeeswarm', 'ggmosaic', 'plotly', 'viridis', 'waffle'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'ggrepel', 'iNZightPlots', 'multcomp'

Packages suggested but not available for checking: 'iNZightTools', 'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'haven', 'readr', 'srvyr', 'styler', 'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ioanalysis.Rcheck/00install.out’ for details.
Package required but not available: ‘plotly’

Package suggested but not available for checking: ‘ComplexHeatmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Biostrings’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/io.Rcheck/00install.out’ for details.
Package required but not available: ‘eurostat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'expm', 'fpc', 'Rmixmod'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IPCWK.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ipcwswitch.Rcheck/00install.out’ for details.
Packages required but not available:
  'eeptools', 'gtsummary', 'tidyverse', 'lmtest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IPDfromKM.Rcheck/00install.out’ for details.
Packages required but not available: 'gdistance', 'raster', 'rgeos'

Packages suggested but not available for checking:
  'geoR', 'gstat', 'spatstat', 'rgdal'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Package required but not available: ‘prodlim’

Packages suggested but not available for checking: 'TH.data', 'party'

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

Packages suggested but not available for checking: 'caret', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'phangorn', 'seqinr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'haven', 'raster', 'readr'

Packages suggested but not available for checking:
  'rgdal', 'biglm', 'RSQLite'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'MplusAutomation', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘survey’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IQCC.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'mlr', 'devtools'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘mpath’

Packages suggested but not available for checking:
  'R.rsp', 'DiagrammeR', 'Hmisc'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'GGMncv'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'fBasics', 'imager'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'twang', 'survey', 'rstanarm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DiagrammeR’
Error(s) in re-building vignettes:
  ...
--- re-building ‘example-scripts.Rmd’ using rmarkdown
--- finished re-building ‘example-scripts.Rmd’

--- re-building ‘getting-started-with-irg.Rmd’ using rmarkdown
Quitting from lines 126-180 (getting-started-with-irg.Rmd) 
Error: processing vignette ‘getting-started-with-irg.Rmd’ failed with diagnostics:
there is no package called 'DiagrammeR'
--- failed re-building ‘getting-started-with-irg.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started-with-irg.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IRISMustangMetrics.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/irlba.Rcheck/00install.out’ for details.
Packages required but not available: 'ChemoSpec', 'hyperSpec'

Package suggested but not available for checking: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘MEMSS’
Running examples in ‘IrregLong-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: abacus.plot
> ### Title: Create an abacus plot Creates an abacus plot, depicting visits
> ###   per subject over time
> ### Aliases: abacus.plot
> 
> ### ** Examples
> 
> library(MEMSS)
Error in library(MEMSS) : there is no package called ‘MEMSS’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Irreglong-vignette.Rmd’ using rmarkdown
Quitting from lines 58-63 (Irreglong-vignette.Rmd) 
Error: processing vignette ‘Irreglong-vignette.Rmd’ failed with diagnostics:
there is no package called 'MEMSS'
--- failed re-building ‘Irreglong-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/irr.Rcheck/00install.out’ for details.
Package required but not available: ‘fGarch’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mirt', 'irtoys'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mirt’
Package required but not available: ‘DiagrammeR’

Packages suggested but not available for checking: 'lme4', 'mirt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ltm', 'mirt', 'fastGHQuad'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘biclust’
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'affy', 'Biobase', 'xcms'
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Iscores.Rcheck/00install.out’ for details.
Packages required but not available:
  'geometry', 'maptools', 'raster', 'rgdal', 'virtualspecies'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'irlba'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'qgraph', 'glmnet'

Package suggested but not available for checking: ‘IsingSampler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IsingSampler.Rcheck/00install.out’ for details.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ismev.Rcheck/00install.out’ for details.
Packages required but not available: 'xlsx', 'xlsxjars'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'metR', 'ggrepel', 'qgraph', 'R.utils'

Package suggested but not available for checking: ‘devtools’

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

Packages suggested but not available for checking:
  'dendextend', 'doParallel', 'rasterVis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IsoCI.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/isocir.Rcheck/00install.out’ for details.
Packages required but not available: 'Biobase', 'affy', 'ff'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘vegan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'latticeExtra', 'raster', 'rasterVis', 'spaMM'

Packages suggested but not available for checking:
  'maptools', 'RandomFields', 'rgeos', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/isoSurv.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/isotonic.pen.Rcheck/00install.out’ for details.
Package required but not available: ‘rstan’

Packages suggested but not available for checking: 'ggraph', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'R2jags', 'R2WinBUGS', 'doParallel'

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

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

Packages suggested but not available for checking: 'devtools', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plotly’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/isva.Rcheck/00install.out’ for details.
Packages required but not available: 'raster', 'maptools', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'apTreeshape', 'geiger'

Depends: includes the non-default packages:
  'partitions', 'VGAM', 'MASS', 'ape', 'apTreeshape', 'geiger',
  'gtools'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/itertools.Rcheck/00install.out’ for details.
Packages required but not available:
  'GGally', 'sna', 'tnet', 'networkDynamic'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'NMF', 'pcalg', 'Rgraphviz'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Quitting from lines 45-47 (vignette.Rmd) 
Error: processing vignette ‘vignette.Rmd’ failed with diagnostics:
there is no package called 'NMF'
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggfortify', 'readr', 'ggcorrplot'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/itsadug.Rcheck/00install.out’ for details.
Packages required but not available: 'car', 'forecast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ecospat', 'raster', 'stars'

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

Package suggested but not available for checking: ‘haven’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gurobi’
Package required but not available: ‘AER’

Packages suggested but not available for checking: 'haven', 'MCMCpack'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
ivFixed.formula: no visible global function definition for
  ‘model.matrix’
ivFixed.formula: no visible global function definition for
  ‘model.response’
summary.ivFixed: no visible global function definition for ‘coef’
summary.ivFixed: no visible global function definition for ‘pt’
Undefined global functions or variables:
  coef model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
Package suggested but not available for checking: ‘locClass’
Packages suggested but not available for checking:
  'gurobi', 'cplexAPI', 'future.apply', 'AER'
Packages required but not available: 'AER', 'lmtest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
hausman: no visible global function definition for ‘pchisq’
ivbe: no visible global function definition for ‘cor’
ivbe: no visible global function definition for ‘pt’
ivfixed: no visible global function definition for ‘cor’
ivfixed: no visible global function definition for ‘pt’
ivpan.formula: no visible global function definition for ‘model.matrix’
ivpan.formula: no visible global function definition for
  ‘model.response’
ivrandom: no visible global function definition for ‘cor’
ivrandom: no visible global function definition for ‘pt’
summary.ivpan: no visible global function definition for ‘printCoefmat’
Undefined global functions or variables:
  cor model.matrix model.response pchisq printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.matrix", "model.response", "pchisq",
             "printCoefmat", "pt")
to your NAMESPACE file.
Packages required but not available: 'lmtest', 'AER'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'lmtest'

Packages suggested but not available for checking: 'AER', 'effects'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘bit64’
Error(s) in re-building vignettes:
  ...
--- re-building ‘ivs.Rmd’ using rmarkdown
Quitting from lines 47-51 (ivs.Rmd) 
Error: processing vignette ‘ivs.Rmd’ failed with diagnostics:
there is no package called 'bit64'
--- failed re-building ‘ivs.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘ahaz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'forecast', 'lmtest'
Running examples in ‘ivx-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ac_test
> ### Title: Autocorrelation tests
> ### Aliases: ac_test
> 
> ### ** Examples
> 
> obj <- ivx(hpi ~ cpi + def + int + log(res), data = ylpc)
> lmtest::bgtest(hpi ~ cpi + def + int + log(res), data = ylpc)
Error in loadNamespace(x) : there is no package called ‘lmtest’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ivx)
  > 
  > test_check("ivx")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 35 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-ivx-ar.R:9:3): ivx_ar univariate ────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'forecast'
  Backtrace:
      ▆
   1. ├─ivx::ivx_ar(hpi ~ inv, ylpc, ar = "forecast") at test-ivx-ar.R:9:2
   2. │ └─ivx::ivx_ar_fit(...)
   3. └─base::loadNamespace(x)
   4.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   5.     └─base withOneRestart(expr, restarts[[1L]])
   6.       └─base doWithOneRestart(return(expr), restart)
  ── Error (test-ivx-ar.R:24:3): ar estimation is identical ──────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'forecast'
  Backtrace:
      ▆
   1. ├─ivx::ivx_ar(...) at test-ivx-ar.R:24:2
   2. │ └─ivx::ivx_ar_fit(...)
   3. └─base::loadNamespace(x)
   4.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   5.     └─base withOneRestart(expr, restarts[[1L]])
   6.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 35 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/iWeigReg.Rcheck/00install.out’ for details.
Package required but not available: ‘fda’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'tm', 'xmlconvert'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package required but not available: ‘imputeYn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DescTools', 'mvp', 'multicool', 'gmpoly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fBasics', 'Benchmarking', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ClusterR', 'irlba'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'ICS', 'ICSNP'
Running examples in ‘JADE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: multscatter
> ### Title: Function to Compute Several Scatter Matrices for the Same Data
> ### Aliases: multscatter
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> # example requires the packages ICS and ICSNP
> library(ICSNP)
Error in library(ICSNP) : there is no package called ‘ICSNP’
Execution halted
Packages required but not available: 'R2jags', 'rjags'

Package suggested but not available for checking: ‘R.utils’

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

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
Packages required but not available:
  'rjags', 'R2jags', 'tidyverse', 'mcmcplots'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/JASPAR.Rcheck/00install.out’ for details.
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:24: warning: The macro `AC_HEADER_STDC' is obsolete.
  configure.ac:24: You should run autoupdate.
  ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from...
  configure.ac:24: the top level
  configure.ac:30: warning: The macro `AC_HEADER_TIME' is obsolete.
  configure.ac:30: You should run autoupdate.
  ./lib/autoconf/headers.m4:743: AC_HEADER_TIME is expanded from...
  configure.ac:30: the top level
  configure.ac:34: warning: The macro `AC_TYPE_SIGNAL' is obsolete.
  configure.ac:34: You should run autoupdate.
  ./lib/autoconf/types.m4:776: AC_TYPE_SIGNAL is expanded from...
  configure.ac:34: the top level
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  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'.
Package required but not available: ‘GA’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/jeek.Rcheck/00install.out’ for details.
Packages required but not available: 'readr', 'imputeTS', 'modeest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'org.Hs.eg.db', 'AnnotationDbi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xts', 'fPortfolio', 'caret'

Packages suggested but not available for checking:
  'DescTools', 'fAssets', 'fBasics', 'forecast', 'FRAPO', 'iClick',
  'quantmod', 'rugarch', 'timeSeries', 'timetk'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/JGEE.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/JGL.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/JGR.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘jiebaR’
Package suggested but not available for checking: ‘devtools’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/jiebaR.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'randtoolbox', 'marqLevAlg'

Package suggested but not available for checking: ‘lcmm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'expm', 'lvm4net'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/JMbayes2.Rcheck/00install.out’ for details.
Packages required but not available:
  'doParallel', 'rstan', 'jagsUI', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
JBTest: no visible global function definition for ‘pchisq’
generateSignificance: no visible global function definition for ‘pnorm’
packages: no visible global function definition for ‘install.packages’
shift: no visible global function definition for ‘tail’
shift: no visible global function definition for ‘head’
splitBy: no visible global function definition for ‘head’
Undefined global functions or variables:
  head install.packages pchisq pnorm tail
Consider adding
  importFrom("stats", "pchisq", "pnorm")
  importFrom("utils", "head", "install.packages", "tail")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/jmotif.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/JM.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'agricolae', 'coin'
Packages required but not available:
  'car', 'multcomp', 'vcd', 'vcdExtra', 'GGally', 'BayesFactor',
  'afex', 'ggrepel'

Packages suggested but not available for checking: 'exact2x2', 'semPlot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'jmv', 'haven'
Error(s) in re-building vignettes:
  ...
--- re-building ‘jmvReadWrite.Rmd’ using rmarkdown

Attaching package: 'jmvReadWrite'

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

    ToothGrowth

Quitting from lines 77-92 (jmvReadWrite.Rmd) 
Error: processing vignette ‘jmvReadWrite.Rmd’ failed with diagnostics:
there is no package called 'jmv'
--- failed re-building ‘jmvReadWrite.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
RE.ADT: no visible global function definition for ‘sd’
RE.ADT: no visible global function definition for ‘pnorm’
RE.Johnson: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm sd
Consider adding
  importFrom("stats", "pnorm", "sd")
to your NAMESPACE file.
Packages required but not available:
  'cobs', 'doParallel', 'lme4', 'randtoolbox'

Packages suggested but not available for checking: 'JM', 'joineR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/joineR.Rcheck/00install.out’ for details.
Packages required but not available: 'glmnet', 'palasso', 'cornet'

Packages which this enhances but not available for checking:
  'earth', 'MRCE', 'remMap', 'mcen', 'GPM', 'RMTL', 'MTPS'

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

Packages suggested but not available for checking: 'ggpubr', 'doFuture'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/joint.Cox.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'JGL', 'brainR'

See section ‘The DESCRIPTION file’ 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.
binteg: no visible global function definition for ‘contourLines’
binteg: no visible global function definition for ‘approx’
binteg: no visible global function definition for ‘par’
plot1: no visible global function definition for ‘par’
plot1: no visible global function definition for ‘rect’
plot1: no visible global function definition for ‘axis’
plot1: no visible global function definition for ‘contour’
plot1: no visible global function definition for ‘contourLines’
plot1: no visible binding for global variable ‘approx’
plot1: no visible global function definition for ‘lines’
plot1: no visible global function definition for ‘text’
plot2: no visible global function definition for ‘abline’
plot2: no visible global function definition for ‘lines’
plot2: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline approx axis contour contourLines legend lines par rect text
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "abline", "axis", "contour", "legend", "lines",
             "par", "rect", "text")
  importFrom("stats", "approx")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'PSCBS', 'R.cache', 'changepoint'
Packages required but not available:
  'timeSeries', 'rChoiceDialogs', 'R.utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘mitml’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'SpATS', 'fds', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'onion', 'emulator'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/JoSAE.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/jose.Rcheck/00install.out’ for details.
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/JPEN.Rcheck/00install.out’ for details.
Package required but not available: ‘leaflet’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/jrich.Rcheck/00install.out’ for details.
Packages required but not available: 'mirt', 'irr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘doParallel’

Packages suggested but not available for checking:
  'raster', 'rgdal', 'boral', 'Hmsc', 'snowfall'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'mediation', 'processR'
Running ‘testthat.R’ [32s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(JSmediation)
  > 
  > test_check("JSmediation")
  Starting 2 test processes
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 89 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-compute_indirect_effect_for.R:53:3): JSmediation approach is consistent with the {mediation} approach (Mod = 1) ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'mediation'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-compute_indirect_effect_for.R:53:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base withOneRestart(expr, restarts[[1L]])
   4.       └─base doWithOneRestart(return(expr), restart)
  ── Error (test-compute_indirect_effect_for.R:92:3): JSmediation approach is consistent with the {processR} approach (Mod = -1, 0, 1) ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'processR'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-compute_indirect_effect_for.R:92:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base withOneRestart(expr, restarts[[1L]])
   4.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 89 ]
  Error: Test failures
  Execution halted
Packages required but not available:
  'jstable', 'labelled', 'GGally', 'haven', 'survey', 'jskm', 'survC1',
  'survIDINRI', 'timeROC', 'Hmisc', 'readr', 'ggpubr', 'epiDisplay'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/JSM.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/jSonarR.Rcheck/00install.out’ for details.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Errors in running code in vignettes:
when running code in ‘json-aaquickstart.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?
when running code in ‘json-apis.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?
when running code in ‘json-paging.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘json-aaquickstart.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘json-apis.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘json-paging.Rmd’ using ‘UTF-8’... failed to complete the test
Packages required but not available: 'bit64', 'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lme4', 'labelled', 'tableone', 'coxme', 'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'furrr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'broom.mixed', 'lme4', 'lmerTest', 'pbkrtest', 'survey', 'weights'

Packages which this enhances but not available for checking:
  'brms', 'quantreg', 'rstanarm'
qtls: no visible global function definition for ‘quantile’
qtls: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm quantile
Consider adding
  importFrom("stats", "pnorm", "quantile")
to your NAMESPACE file.
Package required but not available: ‘xts’

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Package required but not available: ‘SwimmeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/junctions.Rcheck/00install.out’ for details.
Package required but not available: ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BayesFactor', 'Superpower'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggpubr', 'rms', 'quantreg', 'lme4'

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
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'clustMD', 'Hmisc'
Packages required but not available: 'sqldf', 'biomaRt', 'KEGGgraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rglpk', 'CVXR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'affy', 'Biobase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘irr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kappalab.Rcheck/00install.out’ for details.
Packages required but not available: 'maptools', 'rgeos'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/karaoke.Rcheck/00install.out’ for details.
Package required but not available: ‘gganimate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'MVN', 'tseries', 'forecast', 'missForest', 'nonlinearTseries'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kayadata.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kazaam.Rcheck/00install.out’ for details.
Package required but not available: ‘snowfall’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘doParallel’

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

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

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

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

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'univariateML', 'EQL'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'qrng', 'cctools', 'kdecopula', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  /usr/include/c++/12/array:61:36: warning: array subscript 18446744073709551615 is above array bounds of ‘std::__array_traits<double, 1>::_Type’ {aka ‘const double [1]’} [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kdtools.Rcheck/00install.out’ for details.
Running examples in ‘kedd-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dkde
> ### Title: Derivatives of Kernel Density Estimator
> ### Aliases: dkde dkde.default print.dkde
> ### Keywords: smooth nonparametric density derivative
> 
> ### ** Examples
> 
> ## EXAMPLE 1:  Simple example of a Gaussian density derivative
> 
> x <- rnorm(100)
> dkde(x,deriv.order=0)  ## KDE of f
Error in kernel == "epanechnikov" && r >= 3 : 
  'length = 8' in coercion to 'logical(1)'
Calls: dkde -> dkde.default
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rnw’ using Sweave
--- finished re-building ‘intro.Rnw’

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

Error: processing vignette ‘kedd.Rnw’ failed with diagnostics:
 chunk 8 
Error in kernel == "epanechnikov" && r >= 3 : 
  'length = 8' in coercion to 'logical(1)'

--- failed re-building ‘kedd.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'Hmisc', 'raster', 'xts'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lme4', 'metafor'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ltm', 'equateIRT', 'mirt'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kerdiest.Rcheck/00install.out’ for details.
Packages required but not available: 'doParallel', 'doFuture'

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

Packages suggested but not available for checking: 'ks', 'cramer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ks', 'sparr', 'fitdistrplus', 'GB2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'benchmarkme', 'Hmisc', 'rgdal', 'wordspace'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'GA'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘org.Hs.eg.db’
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'future.apply', 'ggrepel'

Package suggested but not available for checking: ‘readtext’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘epade’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Keyboard.Rcheck/00install.out’ for details.
Package required but not available: ‘sna’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'caret', 'doParallel', 'semPlot', 'semTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Error(s) in re-building vignettes:
  ...
--- re-building ‘KFAS.Rnw’ using knitr
Quitting from lines 633-638 (KFAS.Rnw) 
Error: processing vignette ‘KFAS.Rnw’ failed with diagnostics:
there is no package called 'lme4'
--- failed re-building ‘KFAS.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kfda.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘dse’
Packages required but not available: 'fdapace', 'fda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kgc.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggraph’
Packages required but not available:
  'rio', 'Biostrings', 'Rsamtools', 'rtracklayer'

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kin.cohort.Rcheck/00install.out’ for details.
Packages required but not available:
  'readr', 'ggrepel', 'fitdistrplus', 'plotly'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kinship2.Rcheck/00install.out’ for details.
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Bessel', 'kelvin'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'knockoff', 'doParallel'

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

Package which this enhances but not available for checking: ‘ClustVarLV’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘rkward’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/klausuR.Rcheck/00install.out’ for details.
Package required but not available: ‘glmnet’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘emplik’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
dscore: no visible global function definition for ‘glm’
dscore: no visible binding for global variable ‘binomial’
dscore: no visible global function definition for ‘pnorm’
pearson.group: no visible global function definition for ‘cor’
spearman.group: no visible global function definition for ‘cor’
sscore: no visible global function definition for ‘glm’
sscore: no visible binding for global variable ‘binomial’
sscore: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  binomial cor glm pnorm
Consider adding
  importFrom("stats", "binomial", "cor", "glm", "pnorm")
to your NAMESPACE file.
Package suggested but not available for checking: ‘dendextend’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘kmer-vignette.Rmd’ using rmarkdown
Quitting from lines 140-160 (kmer-vignette.Rmd) 
Error: processing vignette ‘kmer-vignette.Rmd’ failed with diagnostics:
there is no package called 'dendextend'
--- failed re-building ‘kmer-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'clv', 'longitudinalData', 'kml'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'clv', 'longitudinalData'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'longitudinalData', 'kml'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
C_zero : <anonymous>: no visible global function definition for ‘runif’
get_extra_centroid_index: no visible global function definition for
  ‘head’
get_within_cluster_ss: no visible global function definition for
  ‘aggregate’
kmod: no visible global function definition for ‘head’
kmod: no visible global function definition for ‘tail’
Undefined global functions or variables:
  aggregate head runif tail
Consider adding
  importFrom("stats", "aggregate", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘pammtools’

Package suggested but not available for checking: ‘devtools’

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
Packages suggested but not available for checking: 'mapproj', 'maptools'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘R.oo’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'showtext', 'styler'
benchmark.patchwork.copula : <anonymous> : <anonymous>: no visible
  global function definition for ‘rbeta’
benchmark.patchwork.copula : <anonymous> : <anonymous>: no visible
  global function definition for ‘runif’
calculate.power : <anonymous>: no visible binding for global variable
  ‘quantile’
generate.benchmark.data: no visible global function definition for
  ‘runif’
generate.benchmark.data: no visible global function definition for
  ‘rnorm’
generate.benchmark.data: no visible global function definition for
  ‘rbinom’
generate.patchwork.copula: no visible global function definition for
  ‘rbeta’
generate.patchwork.copula: no visible global function definition for
  ‘runif’
novelTest.chisq: no visible global function definition for ‘pchisq’
novelTest.chisq4nn: no visible global function definition for ‘pchisq’
optimise.copula.mi : <anonymous>: no visible global function definition
  for ‘optimize’
power.plot: no visible global function definition for ‘axis’
power.plot : <anonymous>: no visible global function definition for
  ‘points’
power.plot: no visible global function definition for ‘legend’
roc.plot: no visible global function definition for ‘colorRampPalette’
roc.plot : <anonymous> : <anonymous>: no visible global function
  definition for ‘points’
run.tests : <anonymous> : <anonymous>: no visible global function
  definition for ‘runif’
Undefined global functions or variables:
  axis colorRampPalette legend optimize pchisq points quantile rbeta
  rbinom rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "legend", "points")
  importFrom("stats", "optimize", "pchisq", "quantile", "rbeta",
             "rbinom", "rnorm", "runif")
to your NAMESPACE file.
Packages required but not available: 'forecast', 'doParallel'

Package suggested but not available for checking: ‘tseries’

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

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

Packages suggested but not available for checking: 'RPtests', 'doParallel'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fossil', 'vegan'

Package suggested but not available for checking: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'glmnet', 'knockoff'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/KODAMA.Rcheck/00install.out’ for details.
Package required but not available: ‘xts’

Package suggested but not available for checking: ‘tstools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/KOGMWU.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘broom.mixed’

Packages suggested but not available for checking:
  'pbkrtest', 'devtools', 'lme4', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'koRpus', 'sylly.en'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'tm', 'koRpus.lang.de', 'koRpus.lang.en', 'koRpus.lang.es',
  'koRpus.lang.fr', 'koRpus.lang.it', 'koRpus.lang.nl',
  'koRpus.lang.pt', 'koRpus.lang.ru'

Package which this enhances but not available for checking: ‘rkward’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/koRpus.Rcheck/00install.out’ for details.
Package required but not available: ‘glmnet’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Kpart.Rcheck/00install.out’ for details.
Packages required but not available: 'pcalg', 'graph'

Package suggested but not available for checking: ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/KPC.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
image.kriging: no visible global function definition for ‘heat.colors’
image.kriging: no visible global function definition for ‘image’
kriging: no visible global function definition for ‘lm’
plot.kriging: no visible global function definition for ‘curve’
Undefined global functions or variables:
  curve heat.colors image lm
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "curve", "image")
  importFrom("stats", "lm")
to your NAMESPACE file.
Packages required but not available: 'randtoolbox', 'anMC'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/krm.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kSamples.Rcheck/00install.out’ for details.
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘KSEA Bar Plot.tiff’ ‘KSEA Kinase Scores.csv’
  ‘KSEA.Merged.Heatmap.png’ ‘Kinase-Substrate Links.csv’
Packages suggested but not available for checking: 'FactoClass', 'LICORS'
kselection: no visible global function definition for ‘txtProgressBar’
kselection: no visible global function definition for
  ‘setTxtProgressBar’
plot.Kselection: no visible global function definition for ‘lines’
plot.Kselection: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend lines setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘expm’

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

Package suggested but not available for checking: ‘geometry’

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

Package suggested but not available for checking: ‘kst’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rgraphviz’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kst.Rcheck/00install.out’ for details.
Package required but not available: ‘GSE’

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
Package required but not available: ‘expm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rockchalk’
Package required but not available: ‘hydroGOF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'R.rsp', 'lme4', 'Hmisc', 'doParallel', 'survey'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kzs.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘raster’
Running ‘testthat.R’ [4s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("L0Learn")
  Loading required package: L0Learn
  [ FAIL 1 | WARN 0 | SKIP 47 | PASS 0 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (47)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_L0Learn_bounds.R:4:1): (code run outside of `test_that()`) ──────
  <packageNotFoundError/error/condition>
  Error in `library("raster")`: there is no package called 'raster'
  Backtrace:
      ▆
   1. └─base::library("raster") at test_L0Learn_bounds.R:4:0
  
  [ FAIL 1 | WARN 0 | SKIP 47 | PASS 0 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘mixtools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/L1pack.Rcheck/00install.out’ for details.
Packages required but not available: 'caret', 'glmnet', 'cvTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/l2boost.Rcheck/00install.out’ for details.
Package required but not available: ‘fGarch’

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

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

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘optpart’

Package which this enhances but not available for checking: ‘vegan’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/labdsv.Rcheck/00install.out’ for details.
Package required but not available: ‘haven’

Package suggested but not available for checking: ‘questionr’

Package which this enhances but not available for checking: ‘memisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package vignette with placeholder title ‘Vignette Title’:
  ‘labelrank.Rmd’
Package suggested but not available for checking: ‘Hmisc’
Error(s) in re-building vignettes:
  ...
--- re-building ‘labelVector.Rmd’ using knitr
Quitting from lines 124-133 (labelVector.Rmd) 
Error: processing vignette ‘labelVector.Rmd’ failed with diagnostics:
there is no package called 'Hmisc'
--- failed re-building ‘labelVector.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'maptools', 'rgdal', 'rgeos', 'spdep'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rcmdr’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LabRS.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘FrF2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘labsimplex.Rmd’ using rmarkdown
Loading required package: FrF2
Please install FrF2 package
Quitting from lines 94-99 (labsimplex.Rmd) 
Error: processing vignette ‘labsimplex.Rmd’ failed with diagnostics:
could not find function "FrF2"
--- failed re-building ‘labsimplex.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘segmented’

Package suggested but not available for checking: ‘datapasta’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatstat', 'spatstat.core', 'spatstat.geom', 'spatstat.random'

Packages suggested but not available for checking:
  'maptools', 'raster', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘L1pack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'devtools', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘tgp’

Packages suggested but not available for checking: 'crs', 'DiceOptim'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'partykit', 'spatialreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'vcd', 'car'
Error(s) in re-building vignettes:
  ...
--- re-building ‘hits-by-type.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

Warning: `funs()` was deprecated in dplyr 0.8.0.
Please use a list of either functions or lambdas: 

  # Simple named list: 
  list(mean = mean, median = median)

  # Auto named with `tibble::lst()`: 
  tibble::lst(mean, median)

  # Using lambdas
  list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
`geom_smooth()` using formula 'y ~ x'
--- finished re-building ‘hits-by-type.Rmd’

--- re-building ‘payroll.Rmd’ using rmarkdown
`summarise()` has grouped output by 'teamID'. You can override using the
`.groups` argument.
Quitting from lines 215-219 (payroll.Rmd) 
Error: processing vignette ‘payroll.Rmd’ failed with diagnostics:
there is no package called 'car'
--- failed re-building ‘payroll.Rmd’

--- re-building ‘run-scoring-trends.Rmd’ using rmarkdown
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
--- finished re-building ‘run-scoring-trends.Rmd’

--- re-building ‘strikeoutsandhr.Rmd’ using rmarkdown
Quitting from lines 29-33 (strikeoutsandhr.Rmd) 
Error: processing vignette ‘strikeoutsandhr.Rmd’ failed with diagnostics:
there is no package called 'car'
--- failed re-building ‘strikeoutsandhr.Rmd’

--- re-building ‘vignette-intro.Rmd’ using rmarkdown
--- finished re-building ‘vignette-intro.Rmd’

SUMMARY: processing the following files failed:
  ‘payroll.Rmd’ ‘strikeoutsandhr.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘R2jags’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LakeMetabolizer.Rcheck/00install.out’ for details.
Packages required but not available: 'rgdal', 'raster', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
‘library’ or ‘require’ calls in package code:
  ‘GPArotation’ ‘mice’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
angoff: no visible global function definition for ‘cov2cor’
angoff: no visible global function definition for ‘runif’
cov.lambda4: no visible global function definition for ‘cov2cor’
cov.lambda4: no visible global function definition for ‘median’
guttman: no visible global function definition for ‘cov2cor’
impute.cov: no visible global function definition for ‘cov’
impute.cov: no visible global function definition for ‘complete’
impute.cov: no visible global function definition for ‘mice’
kristof: no visible global function definition for ‘cov2cor’
kristof: no visible global function definition for ‘runif’
lambda1: no visible global function definition for ‘cov2cor’
lambda2: no visible global function definition for ‘cov2cor’
lambda3: no visible global function definition for ‘cov2cor’
lambda3: no visible binding for global variable ‘sd’
lambda5: no visible global function definition for ‘cov2cor’
lambda6: no visible global function definition for ‘cov2cor’
omega.tot: no visible global function definition for ‘cov2cor’
omega.tot: no visible global function definition for ‘factanal’
quant.lambda4: no visible global function definition for ‘cov2cor’
quant.lambda4: no visible global function definition for ‘runif’
quant.lambda4: no visible global function definition for ‘quantile’
raju: no visible global function definition for ‘cov2cor’
raju: no visible global function definition for ‘runif’
user.lambda4: no visible global function definition for ‘runif’
user.lambda4: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  complete cov cov2cor factanal median mice quantile runif sd
Consider adding
  importFrom("stats", "cov", "cov2cor", "factanal", "median", "quantile",
             "runif", "sd")
to your NAMESPACE file.
checkRd: (7) bin.combs.Rd:11-12: \item in \value must have non-empty label
Packages required but not available:
  'car', 'readr', 'imputeTS', 'modeest', 'torch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘vars’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LambertW.Rcheck/00install.out’ for details.
Packages required but not available: 'CDM', 'sirt'

Packages suggested but not available for checking: 'expm', 'STARTS', 'TAM'

Package which this enhances but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Packages required but not available:
  'riskRegression', 'pec', 'prodlim', 'mstate'

Package suggested but not available for checking: ‘JM’

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

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

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

Package suggested but not available for checking: ‘rgeos’

Package which this enhances but not available for checking: ‘stars’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fields', 'splancs', 'RSQLite', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'airway', 'edgeR', 'EnsDb.Hsapiens.v86', 'AnnotationDbi'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'rms', 'Hmisc', 'lme4', 'multcomp', 'lmerTest'
Package required but not available: ‘styler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘R.matlab’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Vignette_for_LA.Rmd’ using rmarkdown
Quitting from lines 25-27 (Vignette_for_LA.Rmd) 
Error: processing vignette ‘Vignette_for_LA.Rmd’ failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘Vignette_for_LA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘rpart.plot’

Packages suggested but not available for checking: 'quantmod', 'tm'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘example.llo’
Package required but not available: ‘xlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'PGEE', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘snowfall’
Package required but not available: ‘glmnet’

Package suggested but not available for checking: ‘covTest’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ltm’
Error(s) in re-building vignettes:
  ...
--- re-building ‘latdiag.Rnw’ using Sweave
Loading required namespace: ltm
Failed with error:  ‘there is no package called ‘ltm’’
Warning in eval(expr, .GlobalEnv) :
  You need to install ltm to rebuild the vignette

Error: processing vignette ‘latdiag.Rnw’ failed with diagnostics:
 chunk 1 
Error in data.class(X) : object ‘LSAT’ not found

--- failed re-building ‘latdiag.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'fMultivar', 'chebpol', 'heatmaply', 'plotly'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ergm', 'sna'

Packages suggested but not available for checking:
  'snowFT', 'heplots', 'ergm.userterms'

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

Packages suggested but not available for checking:
  'devtools', 'lme4', 'longitudinalData', 'kml', 'lcmm', 'mixtools',
  'flexmix', 'fda', 'funFEM', 'akmedoids', 'dtwclust', 'mixAK',
  'qqplotr', 'doParallel', 'caret'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatstat', 'spatstat.geom', 'splancs', 'spdep', 'spatialreg'

Packages suggested but not available for checking: 'devtools', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'mapproj', 'quantreg'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/latticeExtra.Rcheck/00install.out’ for details.
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘latticeExtra’
Package required but not available: ‘DiagrammeR’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Lavash', 'CVXR'

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

Packages suggested but not available for checking:
  'Rgraphviz', 'fields', 'gof', 'graph', 'lava.tobit', 'lavaSearch2',
  'lme4', 'mets', 'quantreg', 'R.rsp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lava', 'doParallel', 'multcomp'

Packages suggested but not available for checking:
  'lme4', 'lmerTest', 'pbkrtest', 'R.rsp', 'riskRegression'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fBasics’
Running examples in ‘lawstat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nig.parameter
> ### Title: Generate Parameters for the Normal Inverse Gaussian (NIG)
> ###   Distribution
> ### Aliases: nig.parameter
> ### Keywords: distribution
> 
> ### ** Examples
> 
> library(fBasics)
Error in library(fBasics) : there is no package called ‘fBasics’
Execution halted
Packages suggested but not available for checking:
  'extRemes', 'fExtremes', 'ismev', 'mev', 'texmex'
Error(s) in re-building vignettes:
  ...
--- re-building ‘lax-vignette.Rmd’ using rmarkdown
Quitting from lines 168-169 (lax-vignette.Rmd) 
Error: processing vignette ‘lax-vignette.Rmd’ failed with diagnostics:
invalid ‘name’ argument
--- failed re-building ‘lax-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'raster', 'stars'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dipsaus’
Package suggested but not available for checking: ‘forecast’
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘lazyData/R/requireData.R’:
  attach(NULL, pos = pos, name = searchDataName)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lazygreedy.Rcheck/00install.out’ for details.
Packages required but not available: 'raster', 'quadmesh'

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
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘bit64’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
lbfgs: no visible global function definition for ‘hasArg’
Undefined global functions or variables:
  hasArg
Consider adding
  importFrom("methods", "hasArg")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lbiassurv.Rcheck/00install.out’ for details.
Packages required but not available: 'survey', 'maxLik', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rms', 'kinship2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggrepel', 'showtext', 'leaflet', 'leaflet.extras'
Packages required but not available: 'poLCA', 'doParallel', 'GA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'hnp', 'doSNOW', 'doRNG'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘temp.float.csv’ ‘temp.result.athena.csv’
Package required but not available: ‘MCMCpack’

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

Packages suggested but not available for checking: 'NormPsy', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lcopula.Rcheck/00install.out’ for details.
Package required but not available: ‘fdapace’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lcpm.Rcheck/00install.out’ for details.
Package required but not available: ‘rjags’

Package suggested but not available for checking: ‘R2WinBUGS’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'quantmod', 'TTR', 'xts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'kSamples', 'car'

Package suggested but not available for checking: ‘doParallel’

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

Package suggested but not available for checking: ‘tosca’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘penalized’
Packages required but not available:
  'chinese.misc', 'highcharter', 'ldatuning', 'plotly', 'textmineR',
  'tm', 'topicmodels'

Package suggested but not available for checking: ‘Rmpfr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ldat.Rcheck/00install.out’ for details.
Packages required but not available: 'topicmodels', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'topicmodels', 'Rmpfr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'mallet', 'topicmodels'
'LazyData' is specified without a 'data' directory
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Packages required but not available: 'genetics', 'snpStats'

Packages suggested but not available for checking:
  'rtracklayer', 'GenomicRanges', 'GenomeInfoDb', 'IRanges', 'vcfR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ecd', 'xts'

Packages suggested but not available for checking: 'depmixS4', 'R.rsp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'caretEnsemble', 'lares', 'glmnet', 'earth', 'Cubist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
ARConfIntEst: no visible global function definition for ‘sd’
PTLinkFunc: no visible global function definition for ‘pnorm’
PTLinkFunc: no visible global function definition for ‘qnorm’
PTMultiPeriodPD: no visible global function definition for ‘uniroot’
PTOnePeriodPD : f: no visible global function definition for ‘pbinom’
PTOnePeriodPD: no visible global function definition for ‘uniroot’
QMMGetRLogitPD: no visible global function definition for ‘ecdf’
QMMPDlinkFunc: no visible global function definition for ‘qnorm’
QMMPlot: no visible global function definition for ‘lines’
QMMPlot: no visible global function definition for ‘legend’
VDBCalibratePD: no visible global function definition for ‘ecdf’
VDBGetK: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  ecdf legend lines pbinom pnorm qnorm sd uniroot
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "ecdf", "pbinom", "pnorm", "qnorm", "sd",
             "uniroot")
to your NAMESPACE file.
Package suggested but not available for checking: ‘dr’
Running examples in ‘LDRTools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AOP
> ### Title: Function to Average Orthogonal Projection Matrices
> ### Aliases: AOP
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> ## Ex.1
> ##
> library(dr)
Error in library(dr) : there is no package called ‘dr’
Execution halted
Packages required but not available: 'doParallel', 'ashr', 'modeest'

Packages suggested but not available for checking:
  'updog', 'VariantAnnotation'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'GA', 'doFuture'
Package required but not available: ‘leaflet’

Packages suggested but not available for checking: 'raster', 'rmapshaper'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'leaflet', 'raster'

Packages suggested but not available for checking:
  'leafgl', 'plainview', 'rgdal', 'stars'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'leaflet', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'leaflet', 'leaflet.extras'

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

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

Package suggested but not available for checking: ‘readr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'leaflet', 'raster', 'rgdal'
'LazyData' is specified without a 'data' directory
Running examples in ‘leaflet.multiopacity-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addOpacityControls
> ### Title: Add Opacity Controls
> ### Aliases: addOpacityControls
> 
> ### ** Examples
> 
> # Load libraries
> library(leaflet)
Error in library(leaflet) : there is no package called ‘leaflet’
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(leaflet.multiopacity)
  > 
  > test_check("leaflet.multiopacity")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-addOpacityControls.R:2:3): addOpacityControls dependencies are included in leaflet map ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'leaflet'
  Backtrace:
      ▆
   1. ├─leaflet.multiopacity::addOpacityControls(leaflet::leaflet()) at test-addOpacityControls.R:2:2
   2. └─base::loadNamespace(x)
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base withOneRestart(expr, restarts[[1L]])
   5.       └─base doWithOneRestart(return(expr), restart)
  ── Error (test-addOpacityControls.R:8:3): addOpacityControls JS function is registered on jsHooks ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'leaflet'
  Backtrace:
      ▆
   1. ├─leaflet.multiopacity::addOpacityControls(leaflet::leaflet()) at test-addOpacityControls.R:8:2
   2. └─base::loadNamespace(x)
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base withOneRestart(expr, restarts[[1L]])
   5.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘usage-leaflet.Rmd’ using rmarkdown
Quitting from lines 18-27 (usage-leaflet.Rmd) 
Error: processing vignette ‘usage-leaflet.Rmd’ failed with diagnostics:
there is no package called 'leaflet'
--- failed re-building ‘usage-leaflet.Rmd’

--- re-building ‘usage-leafletProxy.Rmd’ using rmarkdown
--- finished re-building ‘usage-leafletProxy.Rmd’

SUMMARY: processing the following file failed:
  ‘usage-leaflet.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'leaflet', 'raster', 'rgdal'
'LazyData' is specified without a 'data' directory
Running examples in ‘leaflet.opacity-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addHigherOpacity
> ### Title: Add higher opacity control to map
> ### Aliases: addHigherOpacity
> 
> ### ** Examples
> 
> # Libraries
> library(leaflet)
Error in library(leaflet) : there is no package called ‘leaflet’
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(leaflet.opacity)
  > library(raster)
  Error in library(raster) : there is no package called 'raster'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'raster', 'viridis'

Packages suggested but not available for checking: 'rgdal', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rgdal’
Running examples in ‘leafletR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: leafletR-package
> ### Title: Interactive Web-Maps Based on the Leaflet JavaScript Library
> ### Aliases: leafletR-package leafletR
> ### Keywords: package
> 
> ### ** Examples
> 
> # load example data (Fiji Earthquakes)
> data(quakes)
> 
> # store data in GeoJSON file (just a subset here)
> q.dat <- toGeoJSON(data=quakes[1:99,], dest=tempdir(), name="quakes")
Columns 1 (lat) and 2 (long) detected as latitude and longitude
Error in is.na(data[, lat.lon[1]]) || is.na(data[, lat.lon[2]]) : 
  'length = 99' in coercion to 'logical(1)'
Calls: toGeoJSON -> dfToGeoJSON
Execution halted
Package required but not available: ‘leaflet’

Packages which this enhances but not available for checking:
  'geojsonio', 'mapedit', 'mapview'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘leaflet’
Packages required but not available: 'lidR', 'raster'

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

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

Package suggested but not available for checking: ‘geojsonio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘doMC’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LEANR.Rcheck/00install.out’ for details.
Package required but not available: ‘alabama’

Package suggested but not available for checking: ‘rjags’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘biglm’
Packages required but not available: 'conicfit', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LearnClust.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'haven', 'readODS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyverse’
Error(s) in re-building vignettes:
  ...
--- re-building ‘learningtower_school.Rmd’ using rmarkdown
Quitting from lines 41-81 (learningtower_school.Rmd) 
Error: processing vignette ‘learningtower_school.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘learningtower_school.Rmd’

--- re-building ‘learningtower_student.Rmd’ using rmarkdown
Quitting from lines 48-57 (learningtower_student.Rmd) 
Error: processing vignette ‘learningtower_student.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘learningtower_student.Rmd’

SUMMARY: processing the following files failed:
  ‘learningtower_school.Rmd’ ‘learningtower_student.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'ChemoSpec', 'chemometrics', 'roxut', 'plotly'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Vig_01_Start_Here.Rmd’ using rmarkdown
--- finished re-building ‘Vig_01_Start_Here.Rmd’

--- re-building ‘Vig_02_Conceptual_Intro_PCA.Rmd’ using rmarkdown
Quitting from lines 29-37 (Vig_02_Conceptual_Intro_PCA.Rmd) 
Error: processing vignette ‘Vig_02_Conceptual_Intro_PCA.Rmd’ failed with diagnostics:
there is no package called 'chemometrics'
--- failed re-building ‘Vig_02_Conceptual_Intro_PCA.Rmd’

--- re-building ‘Vig_03_Step_By_Step_PCA.Rmd’ using rmarkdown
Quitting from lines 29-39 (Vig_03_Step_By_Step_PCA.Rmd) 
Error: processing vignette ‘Vig_03_Step_By_Step_PCA.Rmd’ failed with diagnostics:
there is no package called 'chemometrics'
--- failed re-building ‘Vig_03_Step_By_Step_PCA.Rmd’

--- re-building ‘Vig_04_Scores_Loadings.Rmd’ using rmarkdown
--- finished re-building ‘Vig_04_Scores_Loadings.Rmd’

--- re-building ‘Vig_05_Visualizing_PCA_3D.Rmd’ using rmarkdown
Quitting from lines 29-48 (Vig_05_Visualizing_PCA_3D.Rmd) 
Error: processing vignette ‘Vig_05_Visualizing_PCA_3D.Rmd’ failed with diagnostics:
there is no package called 'plotly'
--- failed re-building ‘Vig_05_Visualizing_PCA_3D.Rmd’

--- re-building ‘Vig_06_Math_Behind_PCA.Rmd’ using rmarkdown
Quitting from lines 30-37 (Vig_06_Math_Behind_PCA.Rmd) 
Error: processing vignette ‘Vig_06_Math_Behind_PCA.Rmd’ failed with diagnostics:
there is no package called 'chemometrics'
--- failed re-building ‘Vig_06_Math_Behind_PCA.Rmd’

--- re-building ‘Vig_07_Functions_PCA.Rmd’ using rmarkdown
--- finished re-building ‘Vig_07_Functions_PCA.Rmd’

SUMMARY: processing the following files failed:
  ‘Vig_02_Conceptual_Intro_PCA.Rmd’ ‘Vig_03_Step_By_Step_PCA.Rmd’
  ‘Vig_05_Visualizing_PCA_3D.Rmd’ ‘Vig_06_Math_Behind_PCA.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘phytools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rio’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/leerSIECyL.Rcheck/00install.out’ for details.
Packages required but not available: 'glmmTMB', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘httptest’
Error(s) in re-building vignettes:
  ...
--- re-building ‘attn.Rmd’ using rmarkdown
Quitting from lines 12-16 (attn.Rmd) 
Error: processing vignette ‘attn.Rmd’ failed with diagnostics:
there is no package called 'httptest'
--- failed re-building ‘attn.Rmd’

--- re-building ‘bills.Rmd’ using rmarkdown
Quitting from lines 12-16 (bills.Rmd) 
Error: processing vignette ‘bills.Rmd’ failed with diagnostics:
there is no package called 'httptest'
--- failed re-building ‘bills.Rmd’

--- re-building ‘hansard.Rmd’ using rmarkdown
Quitting from lines 12-16 (hansard.Rmd) 
Error: processing vignette ‘hansard.Rmd’ failed with diagnostics:
there is no package called 'httptest'
--- failed re-building ‘hansard.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 12-15 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
there is no package called 'httptest'
--- failed re-building ‘introduction.Rmd’

--- re-building ‘schedule.Rmd’ using rmarkdown
Quitting from lines 12-16 (schedule.Rmd) 
Error: processing vignette ‘schedule.Rmd’ failed with diagnostics:
there is no package called 'httptest'
--- failed re-building ‘schedule.Rmd’

--- re-building ‘voting.Rmd’ using rmarkdown
Quitting from lines 12-16 (voting.Rmd) 
Error: processing vignette ‘voting.Rmd’ failed with diagnostics:
there is no package called 'httptest'
--- failed re-building ‘voting.Rmd’

SUMMARY: processing the following files failed:
  ‘attn.Rmd’ ‘bills.Rmd’ ‘hansard.Rmd’ ‘introduction.Rmd’
  ‘schedule.Rmd’ ‘voting.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘smooth’

Packages suggested but not available for checking: 'doMC', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'doSNOW', 'Hmisc', 'glmnet', 'lme4'

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

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Matrix.utils', 'sccore'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'bipartite', 'devtools', 'multinet'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [9s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("leiden")
  Unable to set up conda environment r-reticulate
  run in terminal:
  conda init
  conda create -n r-reticulate
  conda environment r-reticulate installed
  Unable to install python modules igraph and leidenalg
  run in terminal:
  conda install -n r-reticulate -c conda-forge vtraag python-igraph pandas umap learn
  python modules igraph and leidenalg installed
  > 
  > test_check("leiden")
  [ FAIL 1 | WARN 0 | SKIP 33 | PASS 0 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • leidenalg not available for testing (33)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_bipartite.R:4:1): (code run outside of `test_that()`) ───────────
  <packageNotFoundError/error/condition>
  Error in `library("bipartite")`: there is no package called 'bipartite'
  Backtrace:
      ▆
   1. └─base::library("bipartite") at test_bipartite.R:4:0
  
  [ FAIL 1 | WARN 0 | SKIP 33 | PASS 0 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘furrr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘raster’

Packages suggested but not available for checking: 'maptools', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘latticeExtra’

Packages suggested but not available for checking: 'haven', 'readODS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lestat.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'raster', 'fields', 'maptools', 'rgdal', 'rgeos'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'tidyverse', 'future.apply'
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Quitting from lines 116-148 (my-vignette.Rmd) 
Error: processing vignette ‘my-vignette.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘my-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'corpustools', 'RSQLite', 'tm'
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Packages suggested but not available for checking:
  'DESeq2', 'SummarizedExperiment', 'airway'
Error(s) in re-building vignettes:
  ...
--- re-building ‘lfc_vignette.Rmd’ using rmarkdown
Quitting from lines 35-44 (lfc_vignette.Rmd) 
Error: processing vignette ‘lfc_vignette.Rmd’ failed with diagnostics:
there is no package called 'DESeq2'
--- failed re-building ‘lfc_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘plm’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lfe.Rcheck/00install.out’ for details.
Packages required but not available: 'forecast', 'tseries'

Packages suggested but not available for checking: 'doMC', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'xts', 'lmomRFA', 'dygraphs', 'latticeExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lgarch.Rcheck/00install.out’ for details.
Packages required but not available:
  'spatstat.geom', 'spatstat.core', 'spatstat', 'raster',
  'RandomFields', 'fields', 'maptools', 'rgeos'

Packages suggested but not available for checking: 'sparr', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'SKAT', 'geeM'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'localgauss', 'ks', 'np', 'tseries'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'RMariaDB', 'RPostgres', 'RSQLite'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘SKAT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘future.apply’
Package suggested but not available for checking: ‘devtools’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Vignette_for_LHD.Rmd’ using rmarkdown
Quitting from lines 26-28 (Vignette_for_LHD.Rmd) 
Error: processing vignette ‘Vignette_for_LHD.Rmd’ failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘Vignette_for_LHD.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘DoE.base’
Packages required but not available: 'phangorn', 'biomaRt', 'arules'

Packages suggested but not available for checking:
  'fpc', 'modeest', 'vegan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/libbib.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘coin’
Running ‘bugfixes.R’ [0s/1s]
  Comparing ‘bugfixes.Rout’ to ‘bugfixes.Rout.save’ ... OK
  Running ‘regtest_ctabs.R’ [0s/1s]
  Comparing ‘regtest_ctabs.Rout’ to ‘regtest_ctabs.Rout.save’ ... OK
  Running ‘regtest_libcoin.R’ [0s/1s]
Running the tests in ‘tests/regtest_libcoin.R’ failed.
Complete output:
  > 
  > library("libcoin")
  > library("coin")
  Error in library("coin") : there is no package called 'coin'
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Libra.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'readr', 'haven'

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

Package suggested but not available for checking: ‘itertools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'raster', 'imager', 'car', 'reldist', 'lidR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'stars'

Packages suggested but not available for checking:
  'geometry', 'gstat', 'rgdal', 'mapview', 'mapedit'

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

Packages suggested but not available for checking:
  'demography', 'forecast', 'StMoMo'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyverse’
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'MortalityTables', 'objectProperties'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LifeTables.Rcheck/00install.out’ for details.
Packages required but not available: 'adlift', 'nlt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lightgbm.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LightningR.Rcheck/00install.out’ for details.
Package required but not available: ‘future.apply’

Package suggested but not available for checking: ‘pavo’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'laGP', 'doParallel'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cond', 'alabama'

Package suggested but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/likelihood.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘devtools’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/likert.Rcheck/00install.out’ for details.
Packages required but not available:
  'car', 'caret', 'glmnet', 'M3C', 'pathview', 'RCy3', 'survminer'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'tm'

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

Packages suggested but not available for checking: 'mlr', 'text2vec'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: processLimeSurveyDropouts
> ### Title: Process LimeSurvey dropouts
> ### Aliases: processLimeSurveyDropouts
> 
> ### ** Examples
> 
> limonaid::processLimeSurveyDropouts(c(1,2,1,1,2,3,2,2,3,2,1));
Error in limonaid::processLimeSurveyDropouts(c(1, 2, 1, 1, 2, 3, 2, 2,  : 
  To process the LimeSurvey dropouts, you need to have both the {ggplot2} and {ggrepel} packages installed. You can install them with:

  install.packages(c('ggplot2', 'ggrepel'));
Execution halted
Packages required but not available: 'ashr', 'DESeq2', 'mashr'

Package suggested but not available for checking: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'annotate', 'org.Mm.eg.db'
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 22-30 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
there is no package called 'annotate'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘diagram’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LindenmayeR.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘fitdistrplus’
Running examples in ‘LindleyR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DLindley
> ### Title: One-Parameter Discrete Lindley Distribution
> ### Aliases: DLindley ddlindley fires pdlindley qdlindley rdlindley
> 
> ### ** Examples
> 
> set.seed(1)
> x <- rdlindley(n = 1000, theta = 1.5)
> plot(table(x) / sum(table(x)))
> points(unique(x),ddlindley(unique(x), theta = 1.5))
> 
> ## fires in Greece data (from Bakouch et al., 2014)
> data(fires)
> library(fitdistrplus)
Error in library(fitdistrplus) : 
  there is no package called ‘fitdistrplus’
Execution halted
Packages required but not available: 'factoextra', 'glmnet', 'sparsevar'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'viridis', 'readr', 'forecast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/linERR.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘devtools’
Package suggested but not available for checking: ‘devtools’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lingmatch.Rcheck/00install.out’ for details.
Packages required but not available: 'leaflet', 'leaflet.minicharts'

Packages suggested but not available for checking: 'rgeos', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'devtools', 'R.utils', 'raster'

Packages suggested but not available for checking:
  'rgdal', 'RSAGA', 'rgrass7'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/linkcomm.Rcheck/00install.out’ for details.
Package required but not available: ‘spBayes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'BGData', 'ff'
Running examples in ‘LinkedMatrix-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ColumnLinkedMatrix-class
> ### Title: A Class for Linking Matrices by Columns or Rows
> ### Aliases: ColumnLinkedMatrix-class RowLinkedMatrix-class
> ### Keywords: classes
> 
> ### ** Examples
> 
> # Create various matrix-like objects that correspond in dimensions
> m1 <- ff::ff(initdata = rnorm(50), dim = c(5, 10))
Error in loadNamespace(x) : there is no package called ‘ff’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Malformed Description field: should contain one or more complete sentences.
gcomb: no visible global function definition for ‘complete.cases’
linkim: no visible global function definition for ‘runif’
missing.dist: no visible global function definition for
  ‘complete.cases’
pgdata1: no visible global function definition for ‘barplot’
pgdata1: no visible global function definition for ‘layout’
pgdata1: no visible global function definition for ‘par’
pgdata1: no visible global function definition for ‘rainbow’
singim: no visible global function definition for ‘complete.cases’
singim: no visible global function definition for ‘runif’
Undefined global functions or variables:
  barplot complete.cases layout par rainbow runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "barplot", "layout", "par")
  importFrom("stats", "complete.cases", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
gen.lms: no visible global function definition for ‘na.omit’
plot.idf: no visible global function definition for ‘mtext’
plot.idf: no visible global function definition for ‘points’
plot.idf: no visible global function definition for ‘segments’
plot.idf: no visible global function definition for ‘ftable’
plot.idf: no visible global function definition for ‘image’
plot.idf: no visible global function definition for ‘gray’
plot.idf: no visible global function definition for ‘abline’
plot.s.linlir: no visible global function definition for ‘mtext’
plot.s.linlir: no visible global function definition for ‘polygon’
plot.s.linlir: no visible global function definition for ‘points’
plot.s.linlir: no visible global function definition for ‘curve’
s.linlir: no visible global function definition for ‘na.omit’
s.linlir: no visible global function definition for ‘dbinom’
s.linlir: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  abline curve dbinom ftable gray image mtext na.omit pchisq points
  polygon segments
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "curve", "image", "mtext", "points",
             "polygon", "segments")
  importFrom("stats", "dbinom", "ftable", "na.omit", "pchisq")
to your NAMESPACE file.
Rd file 'idf.Rd':
  \usage lines wider than 90 characters:
     plot(x, y=NULL, ..., var = NULL, typ="hist", k.x = 1, k.y = 1, inf.margin=10, p.cex=1, col.lev=15, plot.grid=FALSE, x.adj = 0.5, x.padj ... [TRUNCATED]
  \examples lines wider than 100 characters:
     plot(pm.idf, typ="draft", k.x=10, k.y=20, p.cex=0.35, x.adj=0.5, x.padj=4, y.las=0, y.adj=0.5, y.padj=-4, x.lab="temperature", y.lab="p ... [TRUNCATED]

Rd file 's.linlir.Rd':
  \usage lines wider than 90 characters:
     plot(x, y=NULL, ..., typ, para.typ="polygon", b.grid=500, nb.func=1000, seed.func=NULL, pl.lrm=TRUE, pl.band=FALSE, lrm.col="blue", pl. ... [TRUNCATED]
  \examples lines wider than 100 characters:
     plot(test, typ="lrm", lrm.col="red", pl.band=TRUE, pl.dat=TRUE, pl.dat.typ="draft",k.x=10, k.y=10, y.las=1, y.adj=6)

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/linprog.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'AER', 'gam'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LinRegInteractive.Rcheck/00install.out’ for details.
Package required but not available: ‘elasticnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘doParallel’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
getMatrix : <anonymous>: 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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/listdtr.Rcheck/00install.out’ for details.
Skipping vignette re-building
Packages suggested but not available for checking: 'R.utils', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'magic', 'gamlss.dist', 'arm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘RSQLite’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘stylo’
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'mlr', 'forestmodel'

Packages suggested but not available for checking: 'glmnet', 'mda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'glmnetUtils', 'lme4'

Package suggested but not available for checking: ‘caret’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'MCMCpack'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'partykit', 'survey', 'reghelper'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
lm.beta: no visible global function definition for ‘coef’
lm.beta: no visible global function definition for ‘model.matrix’
lm.beta: no visible global function definition for ‘model.frame’
Undefined global functions or variables:
  coef model.frame model.matrix
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lm.br.Rcheck/00install.out’ for details.
Packages required but not available: 'multcomp', 'sommer'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'MEMSS', 'mlmRev', 'gamm4', 'pbkrtest', 'car', 'rr2', 'semEff'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lme4.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lmec.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'scdhlm', 'mlmRev', 'lme4', 'merDeriv'
Running examples in ‘lmeInfo-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: g_mlm
> ### Title: Calculates adjusted mlm effect size
> ### Aliases: g_mlm
> 
> ### ** Examples
> 
> 
> library(nlme)
> data(Bryant2016, package = "lmeInfo")
> Bryant2016_RML1 <- lme(fixed = outcome ~ treatment,
+                        random = ~ 1 | school/case,
+                        correlation = corAR1(0, ~ session | school/case),
+                        data = Bryant2016)
> Bryant2016_g1 <- g_mlm(Bryant2016_RML1, p_const = c(0,1), r_const = c(1,1,0,1),
+                        infotype = "expected", returnModel = TRUE)
> summary(Bryant2016_g1)
                                           est      se
Tau.school.school.var((Intercept))     105.619 285.200
Tau.case.case.var((Intercept))           0.000 632.159
cor_params                               0.978   0.015
sigma_sq                              1058.302 678.388
total variance                        1163.921 366.515
(Intercept)                             84.571   9.684
treatmenttreatment                      16.425   2.975
treatment effect at a specified time    16.425   2.975
unadjusted effect size                   0.481   0.122
adjusted effect size                     0.463   0.118
degree of freedom                       20.169        
constant kappa                           0.087        
logLik                               -1133.122        
> print(Bryant2016_g1)
                          est    se
unadjusted effect size  0.481 0.122
adjusted effect size    0.463 0.118
degree of freedom      20.169      
> 
> data(Laski, package = "scdhlm")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘scdhlm’
Calls: data -> find.package
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lmeNB.Rcheck/00install.out’ for details.
Packages required but not available: 'lme4', 'fields'

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

Packages suggested but not available for checking:
  'lme4', 'mlmRev', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘pbkrtest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lmeSplines.Rcheck/00install.out’ for details.
Packages required but not available: 'MultiLCIRT', 'diagram'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'spatstat', 'magic', 'spatstat.geom'

Package suggested but not available for checking: ‘lme4’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lava', 'multcomp'

Packages suggested but not available for checking:
  'AICcmodavg', 'ggpubr', 'Publish', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘copBasic’
Packages suggested but not available for checking:
  'rasterList', 'lmomRFA', 'SPEI'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lmomPi.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lmomRFA.Rcheck/00install.out’ for details.
Packages required but not available: 'genefilter', 'Biobase'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lmreg.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'car', 'strucchange', 'dynlm', 'AER'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lmtest.Rcheck/00install.out’ for details.
Packages required but not available: 'origami', 'SuperLearner'

Package suggested but not available for checking: ‘twang’

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

Packages suggested but not available for checking: 'R.rsp', 'plotly'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lmtest', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'seqinr', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘graph’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LncPath.Rcheck/00install.out’ for details.
Packages required but not available: 'dygraphs', 'xts'

Package suggested but not available for checking: ‘feasts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'OpenStreetMap', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rpart.plot’
‘gs+qpdf’ made some significant size reductions:
     compacted ‘LocalControl-jss-2018.pdf’ from 2.1Mb to 1.8Mb
  consider running tools::compactPDF(gs_quality = "ebook") on these files
Error(s) in re-building vignettes:
  ...
--- re-building ‘LocalControl-jss-2018.Rnw’ using Sweave
Loading required package: data.table
Loading required package: colorspace
Loading required package: RColorBrewer
Loading required package: gridExtra
Loading required package: ggplot2
Loading required package: rpart
Loading required package: rpart.plot
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'rpart.plot'
Installing package into '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages'
(as 'lib' is unspecified)
Warning in install.packages("rpart.plot") :
  ‘lib = "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages"’ is not writable

Error: processing vignette ‘LocalControl-jss-2018.Rnw’ failed with diagnostics:
 chunk 2 (label = init_libs_vars_calcs) 
Error in install.packages("rpart.plot") : unable to install packages

--- failed re-building 'LocalControl-jss-2018.Rnw'

SUMMARY: processing the following file failed:
  'LocalControl-jss-2018.Rnw'

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LocalControlStrategy.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/localgauss.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘sampleSelection’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'partykit'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
AnalyticalOptim: no visible global function definition for ‘optim’
LLConstructor : LL: no visible global function definition for ‘dpois’
MixtureDensity: no visible global function definition for ‘glm’
MixtureDensity : f_hat: no visible global function definition for
  ‘predict’
NullDensity : f0: no visible global function definition for ‘dpois’
Undefined global functions or variables:
  dpois glm optim predict
Consider adding
  importFrom("stats", "dpois", "glm", "optim", "predict")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gam’
Package required but not available: ‘wavethresh’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mosaic’
Package required but not available: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'expectreg', 'quantreg', 'lestat'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘vegan’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/loe.Rcheck/00install.out’ for details.
Packages required but not available: 'metR', 'viridis'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'caretEnsemble', 'rpart.plot'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘logcondens’
Packages required but not available: 'logcondens', 'distr'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'R.utils'
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(logger)
  > 
  > if (identical(Sys.getenv("NOT_CRAN"), "true")) {
  +     test_check('logger')
  + } else {
  +     test_check('logger', filter = '^[a-z]*$')
  + }
  WARN [2022-04-30 15:03:13] Running 'sum(1:10)' as 'Mean(1:10)' failed: 'could not find function "Mean"'
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 168 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-appender.R:59:5): logrotate ─────────────────────────────────────
  Error: Please install the 'R.utils' package to use test_check
  Backtrace:
      ▆
   1. └─logger::log_info(i) at test-appender.R:59:4
   2.   └─logger::log_level(...)
   3.     ├─base::do.call(log_fun, log_arg)
   4.     └─logger `<fn>`(...)
   5.       └─logger appender(...)
   6.         └─logger::fail_on_missing_package("R.utils")
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 168 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'partykit', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LOGICOIL.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LogicReg.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/logihist.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/logistic4p.Rcheck/00install.out’ for details.
Packages required but not available: 'rms', 'speedglm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'fda', 'expm', 'fda.usc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘randtoolbox’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
rloglognorm: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: ‘survey’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/logmult.Rcheck/00install.out’ for details.
LogrankA: no visible global function definition for ‘is.Surv’
LogrankA: no visible global function definition for ‘na.omit’
LogrankA: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  is.Surv na.omit pchisq
Consider adding
  importFrom("stats", "na.omit", "pchisq")
to your NAMESPACE file.
Package suggested but not available for checking: ‘ergm’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lolog.Rcheck/00install.out’ for details.
Packages required but not available: 'irlba', 'robust'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'ff', 'aws'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'magic', 'survminer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lme4', 'glmmTMB', 'bestNormalize', 'car', 'rstatix'

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'AICcmodavg', 'missForest', 'R2jags', 'rjags'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/longitudinal.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ConsensusClusterPlus', 'flexmix', 'StatMatch'

Packages suggested but not available for checking:
  'ggalluvial', 'FactoMineR', 'factoextra', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rpart.plot’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/longRPart2.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lookupTable.Rcheck/00install.out’ for details.
Package required but not available: ‘ggmulti’

Packages suggested but not available for checking: 'GGally', 'zenplots'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'graph', 'scagnostics', 'PairViz', 'rworldmap', 'Rgraphviz'
Package required but not available: ‘loon.ggplot’

Packages suggested but not available for checking: 'ggmulti', 'tidyverse'

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

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LoopAnalyst.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/loop.Rcheck/00install.out’ for details.
Packages required but not available:
  'GenomicRanges', 'IRanges', 'S4Vectors'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'brms', 'rstan', 'rstanarm', 'spdep'
Packages required but not available: 'mirt', 'rms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'clime', 'scio'
Malformed Description field: should contain one or more complete sentences.
Packages required but not available: 'emulator', 'magic'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lori.Rcheck/00install.out’ for details.
Packages required but not available: 'pcaMethods', 'geomorph'

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
Package required but not available: ‘RSQLite’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'orthopolynom', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘doMC’
Checking should be performed on sources prepared by ‘R CMD build’.
Package suggested but not available for checking: ‘dr’
Running examples in ‘LPCM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lpc
> ### Title: Local principal curves
> ### Aliases: lpc
> ### Keywords: smooth multivariate
> 
> ### ** Examples
> 
> 
> data(calspeedflow)
> lpc1 <- lpc(calspeedflow[,3:4])
> plot(lpc1)
> 
> data(mussels, package="dr")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘dr’
Calls: data -> find.package
Execution halted
checkRd: (7) Cgenerate.Rd:19: \item in \value must have non-empty label
checkRd: (7) Ggenerate.Rd:17: \item in \value must have non-empty label
checkRd: (7) Sgenerate.Rd:17: \item in \value must have non-empty label
checkRd: (7) Tgenerate.Rd:17: \item in \value must have non-empty label
checkRd: (7) bw_IMSE.Rd:49: \item in \value must have non-empty label
checkRd: (7) bw_IROT.Rd:49: \item in \value must have non-empty label
checkRd: (7) bw_MSE.Rd:49: \item in \value must have non-empty label
checkRd: (7) bw_ROT.Rd:51: \item in \value must have non-empty label
checkRd: (7) coef.lpbwdensity.Rd:15: \item in \value must have non-empty label
checkRd: (7) coef.lpdensity.Rd:15: \item in \value must have non-empty label
checkRd: (7) confint.lpdensity.Rd:25: \item in \value must have non-empty label
checkRd: (7) lpdensity.plot.Rd:125: \item in \value must have non-empty label
checkRd: (7) normal_dgps.Rd:19: \item in \value must have non-empty label
checkRd: (7) plot.lpdensity.Rd:125: \item in \value must have non-empty label
Packages required but not available: 'raster', 'virtualspecies', 'rgdal'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'doParallel', 'ggpubr', 'lmtest', 'plm'

Package suggested but not available for checking: ‘vars’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lpl.Rcheck/00install.out’ for details.
Package required but not available: ‘flexmix’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
‘library’ or ‘require’ call to ‘Rsymphony’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
mipSolve.Rsymphony: no visible global function definition for
  ‘Rsymphony_solve_LP’
Undefined global functions or variables:
  Rsymphony_solve_LP
Package required but not available: ‘powdist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'BayesGOF', 'glmnet', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'LPGraph', 'LPBkg', 'Hmisc', 'orthopolynom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
learnPattern.default: no visible global function definition for ‘runif’
plot.learnPattern: no visible global function definition for ‘matplot’
plotMDS: no visible global function definition for ‘par’
plotMDS: no visible global function definition for ‘rainbow’
plotMDS: no visible global function definition for ‘pairs’
visualizePattern: no visible global function definition for ‘par’
visualizePattern: no visible global function definition for ‘points’
visualizePattern: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend matplot pairs par points rainbow runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "matplot", "pairs", "par", "points")
  importFrom("stats", "runif")
to your NAMESPACE file.
Package required but not available: ‘orthopolynom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'spatstat.geom', 'quantreg'

Packages suggested but not available for checking: 'qrLMM', 'qrNLMM'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/LRMF3.Rcheck/00install.out’ for details.
Packages required but not available:
  'GeneticsPed', 'quantreg', 'kinship2', 'MCMCglmm', 'R.matlab'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'LS2W', 'spdep', 'RandomFields'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'Hmisc'

Packages suggested but not available for checking:
  'BIFIEsurvey', 'TAM', 'miceadds', 'sirt', 'irr', 'difR', 'kerdiest',
  'glmnet', 'mirt', 'car', 'mitml'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tm’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lsa.Rcheck/00install.out’ for details.
Package required but not available: ‘doParallel’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'LICORS', 'fields', 'gam'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘TSdist’

Package suggested but not available for checking: ‘LSDsensitivity’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'LSDinterface', 'tseries', 'kSamples', 'car', 'randtoolbox'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Lsdv.formula: no visible global function definition for ‘model.frame’
Lsdv.formula: no visible global function definition for ‘model.matrix’
Lsdv.formula: no visible global function definition for
  ‘model.response’
lsdv: no visible global function definition for ‘pf’
summary.Lsdv: no visible global function definition for ‘coef’
summary.Lsdv: no visible global function definition for ‘pt’
Undefined global functions or variables:
  coef model.frame model.matrix model.response pf pt
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix",
             "model.response", "pf", "pt")
to your NAMESPACE file.
legend.lshorth: no visible global function definition for ‘legend’
legend.lshorth: no visible global function definition for ‘strwidth’
legend.lshorth: no visible global function definition for ‘text’
plot.lshorth: no visible global function definition for ‘plot.new’
plot.lshorth: no visible global function definition for ‘plot.window’
plot.lshorth: no visible global function definition for ‘axis’
plot.lshorth: no visible global function definition for ‘title’
plot.lshorth: no visible global function definition for ‘box’
plot.lshorth: no visible global function definition for ‘lines’
plot.lshorth: no visible global function definition for ‘legend’
plot.lshorth: no visible global function definition for ‘strwidth’
plot.lshorth: no visible global function definition for ‘text’
Undefined global functions or variables:
  axis box legend lines plot.new plot.window strwidth text title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "lines", "plot.new",
             "plot.window", "strwidth", "text", "title")
to your NAMESPACE file.
Package required but not available: ‘MCMCpack’

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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lsmeans.Rcheck/00install.out’ for details.
Package required but not available: ‘fBasics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'seqinr', 'bit64', 'R.utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lspls.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'raster', 'rasterVis', 'latticeExtra'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘quantreg’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'irlba', 'rsparse', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘MCMCglmm’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ltable.Rcheck/00install.out’ for details.
Package required but not available: ‘readr’

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

Packages suggested but not available for checking: 'mcmcplots', 'ggmcmc'

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

Packages suggested but not available for checking:
  'SuperLearner', 'tmle', 'arm'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
OC : Lnapprox: no visible global function definition for ‘pnorm’
OC : Lnapprox: no visible global function definition for ‘qnorm’
OC : Lt: no visible global function definition for ‘pt’
OC : Lt: no visible global function definition for ‘qnorm’
OC : OC_emwa2: no visible global function definition for ‘pnorm’
OC : OC_emwa2: no visible global function definition for ‘qnorm’
OC: no visible global function definition for ‘pnorm’
OC: no visible global function definition for ‘qnorm’
cmBE : LAtHy: no visible global function definition for ‘phyper’
cmBE: no visible global function definition for ‘uniroot’
planAOQL : Gderivacex: no visible global function definition for
  ‘pnorm’
planAOQL : Mnk: no visible global function definition for ‘uniroot’
planAOQL : k0AOQL : delta: no visible global function definition for
  ‘pnorm’
planAOQL : alpha0: no visible global function definition for ‘pnorm’
planAOQL : alpha0: no visible global function definition for ‘qnorm’
planAOQL : fMSmodq2: no visible global function definition for
  ‘optimize’
planAOQL : kAOQL: no visible global function definition for ‘uniroot’
planLTPD : nAPPROXL : k0L : g: no visible global function definition
  for ‘qnorm’
planLTPD : nAPPROXL : k0L : h: no visible global function definition
  for ‘qnorm’
planLTPD : nAPPROXL : k0L: no visible global function definition for
  ‘qnorm’
planLTPD : nAPPROXL : alpha0: no visible global function definition for
  ‘pnorm’
planLTPD : nAPPROXL : alpha0: no visible global function definition for
  ‘qnorm’
planLTPD : nAPPROXL: no visible global function definition for
  ‘uniroot’
planLTPD : kEWMA: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  optimize phyper pnorm pt qnorm uniroot
Consider adding
  importFrom("stats", "optimize", "phyper", "pnorm", "pt", "qnorm",
             "uniroot")
to your NAMESPACE file.
Packages required but not available: 'ipred', 'prodlim', 'partykit'

Packages suggested but not available for checking:
  'randomForestSRC', 'LTRCtrees'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'partykit', 'icenReg', 'Icens', 'interval'

Package suggested but not available for checking: ‘rpart.plot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ltsbase.Rcheck/00install.out’ for details.
Packages required but not available: 'fields', 'gstat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rrcov’
Error(s) in re-building vignettes:
  ...
--- re-building ‘example.Rmd’ using rmarkdown
Quitting from lines 28-33 (example.Rmd) 
Error: processing vignette ‘example.Rmd’ failed with diagnostics:
there is no package called 'rrcov'
--- failed re-building ‘example.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘genetics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RPostgreSQL', 'rpostgis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'lme4', 'rjags', 'sommer'
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lucid)
  > 
  > test_check("lucid")
    id P1 P2          P3
  1  A  a -1 3.3175e-140
  2  B  b  0 1.0637e-165
  3  C c   1 1.1279e-157
    id P1 P2
  1  A  a -1
  2  B  b  0
  3  C c   1
                                                                                                                                                  P3
  1 0.0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000332
  2 0                                                                                                                                               
  3 0                                                                                                                                               
        effect variance stddev
   (Intercept)   615.3  24.81 
      Residual    16.17  4.021
  [ FAIL 3 | WARN 4 | SKIP 2 | PASS 19 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • empty test (2)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_vc.R:36:3): lmer ────────────────────────────────────────────────
  Error in `lmer(travel ~ 1 + (1 | Rail), data = Rail)`: could not find function "lmer"
  ── Error (test_vc.R:56:3): glmer ───────────────────────────────────────────────
  Error in `glmer(travel ~ 1 + (1 | Rail), data = Rail, family = gaussian(link = "log"))`: could not find function "glmer"
  ── Error (test_vc.R:97:3): mmer ────────────────────────────────────────────────
  Error in `mmer(travel ~ 1, random = ~Rail, data = Rail)`: could not find function "mmer"
  
  [ FAIL 3 | WARN 4 | SKIP 2 | PASS 19 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lucid_examples.Rmd’ using rmarkdown
Loading required package: lucid
Loading required package: lattice
Quitting from lines 213-216 (lucid_examples.Rmd) 
Error: processing vignette ‘lucid_examples.Rmd’ failed with diagnostics:
could not find function "lmer"
--- failed re-building ‘lucid_examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘glmnet’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'rasterVis'

Packages suggested but not available for checking:
  'caret', 'gsubfn', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'plotly', 'rjags', 'devtools', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
terrestrial.season: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package suggested but not available for checking: ‘rgdal’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test’
Package required but not available: ‘torch’

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

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

Package suggested but not available for checking: ‘manet’

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

Packages suggested but not available for checking: 'devtools', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'qgraph', 'semPlot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘depth’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘doFuture’

Package suggested but not available for checking: ‘sirad’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gWQS', 'gamm4'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘caret’

Packages suggested but not available for checking:
  'adehabitatLT', 'moveHMM', 'DiagrammeR'

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

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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
Packages required but not available: 'rgdal', 'mapdata'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'GenomicRanges', 'GenomicAlignments', 'GenomicFeatures',
  'GenomeInfoDb', 'Rsamtools', 'IRanges'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'icenReg', 'doParallel'

Packages suggested but not available for checking:
  'mixtools', 'coxinterval'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘C50’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dials', 'party', 'recipes', 'rsample'

Packages suggested but not available for checking:
  'adabag', 'BART', 'bartMachine', 'C50', 'doParallel', 'earth',
  'elasticnet', 'glmnet', 'Hmisc', 'mboost', 'mda',
  'ParBayesianOptimization', 'partykit', 'randomForestSRC', 'rms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'etl', 'readr'

Packages suggested but not available for checking: 'RSQLite', 'leaflet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'party', 'plsgenomics', 'st'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mediation', 'emplik'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mada.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘maddison_project_database.Rmd’
Package required but not available: ‘torch’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'metafor', 'R2wd'

Package which this enhances but not available for checking: ‘irr’
‘library’ or ‘require’ calls in package code:
  ‘R2wd’ ‘ggplot2’ ‘metafor’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mads.Rcheck/00install.out’ for details.
Package required but not available: ‘geometry’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'TCGAbiolinks', 'plotly', 'ComplexHeatmap', 'ggbeeswarm',
  'GenomicRanges', 'IRanges', 'readr'

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

Package suggested but not available for checking: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'SeqArray', 'SeqVarTools', 'GMMAT'

Package suggested but not available for checking: ‘doMC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'celestial', 'mapproj'

Package suggested but not available for checking: ‘imager’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/magickGUI.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/magic.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘dittoSeq’
Packages required but not available:
  'coxme', 'doParallel', 'lme4', 'multcomp', 'qqman', 'seqinr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'weights'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘readr’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mailmerge)
  > 
  > test_check("mailmerge")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-mail_merge.R:3:3): (code run outside of `test_that()`) ──────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'readr'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-mail_merge.R:3:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base withOneRestart(expr, restarts[[1L]])
   4.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Malformed Description field: should contain one or more complete sentences.
Package required but not available: ‘R.utils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rrcov', 'GGally', 'sn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘introduction-to-package-majesticr--rmd.Rmd’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rstan', 'INLA'
Package unavailable to check Rd xrefs: ‘INLA’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/malani.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'ggraph', 'Rmpfr'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/malan.Rcheck/00install.out’ for details.
Packages required but not available: 'rgdal', 'raster'

Package suggested but not available for checking: ‘rdhs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MALDIquantForeign.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MALDIrppa.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mallet.Rcheck/00install.out’ for details.
Package required but not available: ‘future.apply’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘readr’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'imager', 'caret'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘kinship2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Mangrove.Rnw’ using Sweave

Error: processing vignette ‘Mangrove.Rnw’ failed with diagnostics:
 chunk 19 
Error in library(kinship2) : there is no package called ‘kinship2’

--- failed re-building ‘Mangrove.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘plotly’

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

Package suggested but not available for checking: ‘R.utils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tm', 'readr'

Packages suggested but not available for checking:
  'R.rsp', 'haven', 'devtools'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ManifoldOptim.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'dygraphs', 'leaflet', 'plotly', 'xts'
Error(s) in re-building vignettes:
  ...
--- re-building ‘manipulateWidgets.Rmd’ using rmarkdown
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette ‘manipulateWidgets.Rmd’ failed with diagnostics:
there is no package called 'dygraphs'
--- failed re-building ‘manipulateWidgets.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘DescTools’
Packages required but not available: 'magic', 'multcomp'

Packages suggested but not available for checking: 'RGtk2', 'GFD'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'haven', 'readr'
Packages required but not available: 'caret', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'nsga2R', 'randtoolbox'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Map2NCBI.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'forecast', 'smooth'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'slippymath', 'leaflet', 'raster'

Packages suggested but not available for checking:
  'ggspatial', 'tigris', 'tidycensus', 'tmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘showtext’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mapdata.Rcheck/00install.out’ for details.
Packages required but not available:
  'MANOVA.RM', 'MultBiplotR', 'car', 'highcharter', 'MVN', 'heplots',
  'vegan', 'rstan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'leafem', 'leaflet', 'leaflet.extras', 'leafpm', 'mapview', 'raster'

Package which this enhances but not available for checking: ‘geojsonio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mapfit.Rcheck/00install.out’ for details.
Packages required but not available: 'gam', 'maptools'

Package suggested but not available for checking: ‘mapproj’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘latticeExtra’
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spruce', 'Seurat', 'ggalluvial', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'DiagrammeR', 'exactextractr', 'SPEI'
Error(s) in re-building vignettes:
  ...
--- re-building ‘terminology.Rmd’ using rmarkdown
--- finished re-building ‘terminology.Rmd’

--- re-building ‘userguide.Rmd’ using rmarkdown
Linking to GEOS 3.10.2, GDAL 3.4.2, PROJ 9.0.0; sf_use_s2() is TRUE

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 205-206 (userguide.Rmd) 
Error: processing vignette ‘userguide.Rmd’ failed with diagnostics:
Creation failed.

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

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘raster’

Packages suggested but not available for checking: 'rgdal', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tmap', 'cartography', 'rgdal', 'leaflet', 'tmaptools', 'leafsync',
  'mapview', 'geojsonio'

Package suggested but not available for checking: ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shapefiles’
Running examples in ‘mapplots-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: draw.shape
> ### Title: Draw shapefiles in an existing plot
> ### Aliases: draw.shape
> 
> ### ** Examples
> 
> library(shapefiles)
Error in library(shapefiles) : there is no package called ‘shapefiles’
Execution halted
Packages required but not available:
  'fields', 'ggpubr', 'smacof', 'dendextend', 'vcfR', 'plotly'

Packages suggested but not available for checking: 'updog', 'polymapR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mapproj.Rcheck/00install.out’ for details.
Package required but not available: ‘flexmix’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rgdal', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'leaflet', 'spocc'

Packages suggested but not available for checking:
  'taxize', 'maptools', 'scrubr'

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

Package suggested but not available for checking: ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'slippymath'

Package suggested but not available for checking: ‘mapview’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mapsf.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'ggspatial', 'leaflet', 'raster', 'slippymath'
Running examples in ‘mapSpain-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addProviderEspTiles
> ### Title: Include base tiles of Spanish public administrations on a
> ###   *leaflet* map
> ### Aliases: addProviderEspTiles providerEspTileOptions
> 
> ### ** Examples
> 
> library(leaflet)
Error in library(leaflet) : there is no package called ‘leaflet’
Execution halted
Running ‘testthat.R’ [43s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mapSpain)
  > 
  > test_check("mapSpain")
  Starting 2 test processes
  [ FAIL 1 | WARN 0 | SKIP 22 | PASS 137 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (17)
  • ggspatial cannot be loaded (1)
  • leaflet cannot be loaded (1)
  • slippymath cannot be loaded (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-esp_getTiles.R:7:3): tiles error ────────────────────────────────
  Error in `esp_getTiles(df)`: slippymath package required for using this function
  Backtrace:
      ▆
   1. ├─testthat::expect_error(esp_getTiles(df), "Only sf and sfc objects allowed") at test-esp_getTiles.R:7:2
   2. │ └─testthat:::expect_condition_matching(...)
   3. │   └─testthat:::quasi_capture(...)
   4. │     ├─testthat .capture(...)
   5. │     │ └─base::withCallingHandlers(...)
   6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   7. └─mapSpain::esp_getTiles(df)
  
  [ FAIL 1 | WARN 0 | SKIP 22 | PASS 137 ]
  Error: Test failures
  Execution halted
Packages suggested but not available for checking: 'mapproj', 'mapdata'
Packages required but not available: 'raster', 'gstat', 'rgdal', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'survey', 'maptools', 'Hmisc'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rgeos', 'spatstat.geom', 'raster', 'spatstat.linnet', 'spatstat'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/maptools.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/maptpx.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/maptree.Rcheck/00install.out’ for details.
Packages required but not available:
  'leafem', 'leaflet', 'raster', 'satellite'

Packages suggested but not available for checking:
  'leaflet.extras2', 'leafsync', 'plainview', 'rgdal', 'stars'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cmrutils', 'fda'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'readr', 'devtools', 'scholar', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'brms', 'ggbeeswarm', 'haven', 'quantreg', 'tidyverse', 'AER',
  'betareg', 'gam', 'glmx', 'itsadug', 'ivreg', 'lme4', 'lmerTest',
  'mclogit', 'plm', 'rms', 'robust', 'robustlmm', 'rstanarm',
  'sampleSelection', 'scam', 'speedglm', 'survey', 'truncreg'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [180s/131s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(marginaleffects)
  > library(margins)
  > 
  > test_check("marginaleffects")
  Starting 2 test processes
  [ FAIL 1 | WARN 0 | SKIP 37 | PASS 417 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • AER cannot be loaded (1)
  • On CRAN (10)
  • betareg cannot be loaded (1)
  • brms cannot be loaded (1)
  • gam cannot be loaded (1)
  • glmx cannot be loaded (1)
  • haven cannot be loaded (1)
  • itsadug cannot be loaded (1)
  • ivreg cannot be loaded (2)
  • lme4 cannot be loaded (2)
  • lmerTest cannot be loaded (1)
  • mclogit cannot be loaded (1)
  • modelbased cannot be loaded (1)
  • plm cannot be loaded (3)
  • quantreg cannot be loaded (1)
  • rms cannot be loaded (1)
  • robust cannot be loaded (1)
  • robustlmm cannot be loaded (1)
  • rstanarm cannot be loaded (1)
  • sampleSelection cannot be loaded (1)
  • scam cannot be loaded (1)
  • speedglm cannot be loaded (1)
  • survey cannot be loaded (1)
  • truncreg cannot be loaded (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-tidy.R:46:5): glance: with modelsummary ───────────────────────
  dim(glance(mfx)) (`actual`) not equal to c(1, 10) (`expected`).
  
    `actual`: 1  9
  `expected`: 1 10
  
  [ FAIL 1 | WARN 0 | SKIP 37 | PASS 417 ]
  Error: Test failures
  Execution halted
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘betareg’
Package suggested but not available for checking: ‘lme4’

Packages which this enhances but not available for checking:
  'AER', 'betareg', 'survey'
Packages suggested but not available for checking:
  'cond', 'csampling', 'nlreg'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/marg.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lme4', 'expm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'doParallel', 'CausalImpact', 'bsts', 'Boom', 'dtw'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘phangorn’

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

Packages suggested but not available for checking:
  'diagram', 'DiagrammeR', 'msm', 'ctmcd'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'metR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'survidm', 'mstate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘haven’
negbin.rel.clust: no visible global function definition for ‘kmeans’
negbin.rel.clust: no visible global function definition for ‘matplot’
negbin.rel.pca: no visible global function definition for ‘princomp’
negbin.rel.pca: no visible global function definition for ‘biplot’
pois.rel.clust: no visible global function definition for ‘kmeans’
pois.rel.clust: no visible global function definition for ‘matplot’
pois.rel.pca: no visible global function definition for ‘princomp’
pois.rel.pca: no visible global function definition for ‘biplot’
sim.negbin: no visible global function definition for ‘rnbinom’
sim.pois: no visible global function definition for ‘rpois’
wt.rel.negbin: no visible global function definition for ‘var’
wt.rel.negbin: no visible global function definition for ‘optimize’
wt.rel.negbin: no visible global function definition for ‘integrate’
wt.rel.pois: no visible global function definition for ‘optimize’
wt.rel.pois: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  biplot integrate kmeans matplot optimize princomp rnbinom rpois var
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "biplot", "integrate", "kmeans", "optimize",
             "princomp", "rnbinom", "rpois", "var")
to your NAMESPACE file.
Packages required but not available:
  'RSQLite', 'gdistance', 'raster', 'adehabitatMA'

Packages suggested but not available for checking:
  'mapdata', 'mapproj', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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

Package suggested but not available for checking: ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mAr.Rcheck/00install.out’ for details.
Package required but not available: ‘earth’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'forecast', 'Hmisc', 'lme4'
Running examples in ‘MARSS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: accuracy.marssMLE
> ### Title: Return accuracy metrics
> ### Aliases: accuracy.marssMLE accuracy.marssPredict
> 
> ### ** Examples
> 
> dat <- t(harborSeal)
> dat <- dat[c(2, 11, 12),]
> train.dat <- dat[,1:12]
> fit <- MARSS(train.dat, model = list(Z = factor(c("WA", "OR", "OR"))))
Success! abstol and log-log tests passed at 79 iterations.
Alert: conv.test.slope.tol is 0.5.
Test with smaller values (<0.1) to ensure convergence.

MARSS fit is
Estimation method: kem 
Convergence test: conv.test.slope.tol = 0.5, abstol = 0.001
Estimation converged in 79 iterations. 
Log-likelihood: 14.98234 
AIC: -13.96467   AICc: -2.887748   
 
                Estimate
A.OR.SouthCoast   0.8952
R.diag            0.0087
U.WA              0.1043
U.OR              0.0569
Q.(WA,WA)         0.0112
Q.(OR,OR)         0.0000
x0.WA             7.3171
x0.OR             6.2970
Initial states (x0) defined at t=0

Standard errors have not been calculated. 
Use MARSSparamCIs to compute CIs and bias estimates.

> 
> library(forecast)
Error in library(forecast) : there is no package called ‘forecast’
Execution halted
Package required but not available: ‘earth’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'devtools', 'JoSAE', 'R.rsp', 'sae'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Errors in running code in vignettes:
when running code in ‘maSAE.Rnw’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘maSAE.Rnw’ using ‘UTF-8’... failed to complete the test
Packages required but not available: 'glmnet', 'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ashr', 'softImpute'

Packages suggested but not available for checking: 'REBayes', 'flashr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tidyverse’
Error(s) in re-building vignettes:
  ...
--- re-building ‘rationale.Rmd’ using rmarkdown
Quitting from lines 19-32 (rationale.Rmd) 
Error: processing vignette ‘rationale.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘rationale.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/massiveGST.Rcheck/00install.out’ for details.
Package required but not available: ‘repmis’

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

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

Package suggested but not available for checking: ‘RItools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Matching.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/matchingR.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'optmatch', 'Matching', 'CBPS', 'glmnet', 'lmtest', 'Rglpk', 'gurobi'
Error(s) in re-building vignettes:
  ...
--- re-building ‘MatchIt.Rmd’ using rmarkdown
Quitting from lines 198-205 (MatchIt.Rmd) 
Error: processing vignette ‘MatchIt.Rmd’ failed with diagnostics:
there is no package called 'lmtest'
--- failed re-building ‘MatchIt.Rmd’

--- re-building ‘assessing-balance.Rmd’ using rmarkdown
 cobalt (Version 4.3.2, Build Date: 2022-01-19)

Attaching package: 'cobalt'

The following object is masked _by_ '.GlobalEnv':

    lalonde

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

    lalonde

--- finished re-building ‘assessing-balance.Rmd’

--- re-building ‘estimating-effects.Rmd’ using rmarkdown
Quitting from lines 169-174 (estimating-effects.Rmd) 
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--- failed re-building ‘estimating-effects.Rmd’

--- re-building ‘matching-methods.Rmd’ using rmarkdown
--- finished re-building ‘matching-methods.Rmd’

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Quitting from lines 79-84 (sampling-weights.Rmd) 
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there is no package called 'lmtest'
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SUMMARY: processing the following files failed:
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Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'rcbsubset', 'coin', 'weights', 'Hmisc'

Package suggested but not available for checking: ‘optmatch’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/matchr.Rcheck/00install.out’ for details.
Package required but not available: ‘survey’

Packages suggested but not available for checking: 'Amelia', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'seriation', 'cba'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Found the following possibly unsafe calls:
File ‘matlab/R/zzz.R’:
  unlockBinding("savedTime", .MatlabNamespaceEnv)

colorbar : colorbar.EO: no visible global function definition for ‘par’
colorbar : colorbar.EO: no visible global function definition for
  ‘axis’
colorbar : colorbar.EO: no visible global function definition for
  ‘axTicks’
colorbar : colorbar.EO: no visible global function definition for ‘box’
colorbar : colorbar.NO: no visible global function definition for
  ‘axis’
colorbar : colorbar.NO: no visible global function definition for
  ‘axTicks’
colorbar : colorbar.NO: no visible global function definition for ‘box’
imagesc : pretty.axp: no visible global function definition for ‘par’
imagesc: no visible global function definition for ‘axis’
imagesc: no visible global function definition for ‘box’
jet.colors: no visible global function definition for ‘rgb’
multiline.plot.colors : get.gca.colororder: no visible global function
  definition for ‘rgb’
std: no visible global function definition for ‘sd’
Undefined global functions or variables:
  axTicks axis box par rgb sd
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axTicks", "axis", "box", "par")
  importFrom("stats", "sd")
to your NAMESPACE file.
Package required but not available: ‘car’

Package suggested but not available for checking: ‘webshot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'forecast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
MAT: no visible global function definition for ‘dev.new’
MAT: no visible global function definition for ‘points’
MAT: no visible global function definition for ‘abline’
MAT: no visible global function definition for ‘text’
MAT: no visible global function definition for ‘legend’
MAT: no visible global function definition for ‘lines’
MAT: no visible global function definition for ‘par’
MAT: no visible global function definition for ‘barplot’
MAT: no visible global function definition for ‘cor’
print.MAT: no visible global function definition for ‘sd’
print.MAT: no visible global function definition for ‘cor’
simM3PL: no visible global function definition for ‘rnorm’
simM3PL: no visible global function definition for ‘runif’
Undefined global functions or variables:
  abline barplot cor dev.new legend lines par points rnorm runif sd
  text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "barplot", "legend", "lines", "par",
             "points", "text")
  importFrom("stats", "cor", "rnorm", "runif", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MatrixExtra.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘doSNOW’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘MBSP’
Package required but not available: ‘TTR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘expm’

Packages which this enhances but not available for checking:
  'graph', 'maptools', 'spdep'
Package unavailable to check Rd xrefs: ‘graph’
'LazyData' is specified without a 'data' directory
Skipping vignette re-building
Packages suggested but not available for checking: 'R.devices', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Packages suggested but not available for checking:
  'car', 'cosinor2', 'PMCMRplus'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Matrix.utils.Rcheck/00install.out’ for details.
Package required but not available: ‘RCLabels’

Package suggested but not available for checking: ‘matsindf’

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

Package suggested but not available for checking: ‘RCLabels’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Rd file 'mat.dissim.Rd':
  \usage lines wider than 90 characters:
     mat.dissim(inFossil, inModern, llMod = c(), modTaxa = c(), llFoss = c(), fosTaxa = c(), numAnalogs = 1, counts = T, sitenames = 1:lengt ... [TRUNCATED]

Rd file 'mat.fossavg.Rd':
  \usage lines wider than 90 characters:
     mat.fossavg(dObj, modEnvCol, fossEnvCol = 0, fossCols = 0, cutoff = 0, distance = -1, wmethod = "none", numanalogs = length(dObj$positi ... [TRUNCATED]

Rd file 'mat.jumprecon.Rd':
  \usage lines wider than 90 characters:
     mat.jumprecon(dObj, modEnvCol, fossEnvCol, cutoff = 0, alpha = NULL, distance = -1, numanalogs = length(dObj$position[, 1]))

Rd file 'mat.mc.Rd':
  \usage lines wider than 90 characters:
     mat.mc(inModern, modTaxa = c(NULL, NULL), probs = c(0.05, 0.025, 0.01, 0.001), freqint = seq(0, 2, 0.02), sampleSize = length(inModern[ ... [TRUNCATED]

Rd file 'mat.roc.Rd':
  \usage lines wider than 90 characters:
     mat.roc(inModern, modTaxa = c(), colClasses = NULL, numAnalogs = 2, rocEvalSeq = seq(0, 2, 0.05), counts = F, aucmethod = "trap")

Rd file 'mat.roc.allpair.Rd':
  \usage lines wider than 90 characters:
     mat.roc.allpair(inModern, modTaxa = c(), colClasses = NULL, numAnalogs = 2, rocEvalSeq = seq(0, 2, 0.05), counts = F, aucmethod = "trap ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Package required but not available: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘utilities.R’
Package required but not available: ‘beastier’

Package suggested but not available for checking: ‘beautier’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MaXact.Rcheck/00install.out’ for details.
Packages required but not available: 'aucm', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mstate', 'MCMCpack'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'CVXR', 'glmnet', 'SIHR'

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

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

Package suggested but not available for checking: ‘dismo’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/maxLik.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘GA’

Package suggested but not available for checking: ‘fUnitRoots’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MaxPro.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘TH.data’
Running examples in ‘maxstat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: maxstat.test
> ### Title: Maximally Selected Rank and Statistics
> ### Aliases: maxstat.test maxstat.test.data.frame maxstat.test.default
> ###   maxstat
> ### Keywords: htest
> 
> ### ** Examples
> 
> 
> set.seed(29)
> 
> x <- sort(runif(20))
> y <- c(rnorm(10), rnorm(10, 2))
> mydata <- data.frame(cbind(x,y))
> 
> mod <- maxstat.test(y ~ x, data=mydata, smethod="Wilcoxon", pmethod="HL",
+                     minprop=0.25, maxprop=0.75, alpha=0.05)
> print(mod)

Maximally selected Wilcoxon statistics using HL

data:  y by x
M = 3.4017, p-value = 0.0009476
sample estimates:
estimated cutpoint 
         0.3621201 

> plot(mod)
> 
> # adjusted for more than one prognostic factor.
> library("survival")
> mstat <- maxstat.test(Surv(time, cens) ~ IPI + MGE, data=DLBCL, 
+                       smethod="LogRank", pmethod="exactGauss", 
+                       abseps=0.01)
> plot(mstat)
> 
> ### sphase
> set.seed(29)
> data("sphase", package = "TH.data")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘TH.data’
Calls: data -> find.package
Execution halted
Package required but not available: ‘aucm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘quickcheck’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(maybe)
  > 
  > test_check("maybe")
  Error in library(quickcheck) : there is no package called 'quickcheck'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Package required but not available: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'leaflet', 'MazamaCoreUtils', 'MazamaSpatialUtils', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'MazamaSpatialUtils', 'MazamaCoreUtils', 'tmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cleangeo', 'MazamaCoreUtils', 'rgdal', 'rgeos', 'rmapshaper'

Package suggested but not available for checking: ‘readr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘map_5.png’ ‘maze_5.html’
Skipping vignette re-building
Packages suggested but not available for checking:
  'doMC', 'gamlss.dist', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘my-vignette.Rmd’
Package suggested but not available for checking: ‘emojifont’
Error(s) in re-building vignettes:
  ...
--- re-building ‘inspiration.Rmd’ using rmarkdown
Quitting from lines 139-146 (inspiration.Rmd) 
Error: processing vignette ‘inspiration.Rmd’ failed with diagnostics:
could not find function "emoji"
--- failed re-building ‘inspiration.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fitdistrplus', 'alabama'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
MI.2: no visible global function definition for ‘xtabs’
RNASeq.Data: no visible binding for global variable ‘quantile’
loc.node: no visible global function definition for ‘head’
loc.node: no visible global function definition for ‘tail’
plotHybrid.Tree: no visible global function definition for ‘par’
plotHybrid.Tree: no visible global function definition for ‘text’
plotHybrid.Tree: no visible global function definition for ‘image’
plotHybrid.Tree: no visible global function definition for ‘grey’
plotHybrid.Tree: no visible global function definition for
  ‘heat.colors’
plotHybrid.Tree: no visible global function definition for ‘head’
plotHybrid.Tree: no visible global function definition for ‘segments’
plotbr: no visible global function definition for ‘segments’
Undefined global functions or variables:
  grey head heat.colors image par quantile segments tail text xtabs
Consider adding
  importFrom("grDevices", "grey", "heat.colors")
  importFrom("graphics", "image", "par", "segments", "text")
  importFrom("stats", "quantile", "xtabs")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MBC.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'sem', 'semTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geometry', 'randtoolbox', 'raster'

Packages suggested but not available for checking: 'fields', 'spsurvey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
cfull: no visible global function definition for ‘combn’
cl: no visible global function definition for ‘combn’
cn: no visible global function definition for ‘combn’
crep: no visible global function definition for ‘combn’
crich: no visible global function definition for ‘combn’
ct: no visible global function definition for ‘combn’
mjaccard: no visible global function definition for ‘combn’
ml: no visible global function definition for ‘combn’
mn: no visible global function definition for ‘combn’
mrep: no visible global function definition for ‘combn’
mrich: no visible global function definition for ‘combn’
msorensen: no visible global function definition for ‘combn’
mt: no visible global function definition for ‘combn’
wnodf: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘chipPCR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'R2jags', 'rjags', 'rgeos'

Packages suggested but not available for checking:
  'overlapping', 'mcmcplots', 'forestplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'R2jags', 'rjags'

Packages suggested but not available for checking:
  'overlapping', 'rgeos', 'Hmisc', 'mcmcplots'

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

Packages suggested but not available for checking:
  'TH.data', 'fields', 'BayesX', 'kangar00'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggforce’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘brglm’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mbrglm.Rcheck/00install.out’ for details.
Packages required but not available: 'dplR', 'Rfast'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fitdistrplus’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mc2d.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Rd file 'VegTypeChanges.Rd':
  \examples lines wider than 100 characters:
     ## vegChanges = VegTypeChanges(ncdf.th <- system.file("netcdf", "WW2100_HadGEM2-ES85_year_sample.nc", PACKAGE = "MC2toPath")path, base. ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘fireFracs.csv’ ‘fireProbabilityMultipliers.txt’
  ‘vegChangeProbabilityMultipliers.txt’
Packages required but not available: 'ggrepel', 'plotly'

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
Packages required but not available:
  'mlr3', 'mlr3pipelines', 'mlr3proba', 'glmnet'

Packages suggested but not available for checking:
  'tidyverse', 'mlr3learners', 'mlr3oml'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'smoothmest'

Package suggested but not available for checking: ‘flare’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mccf1.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mcclust.Rcheck/00install.out’ for details.
getbetap.A: no visible global function definition for ‘pbeta’
getbetap.A: no visible global function definition for ‘cor.test’
Undefined global functions or variables:
  cor.test pbeta
Consider adding
  importFrom("stats", "cor.test", "pbeta")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rglpk’

Packages suggested but not available for checking: 'Rgraphviz', 'cplexAPI'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mcemGLM.Rcheck/00install.out’ for details.
Packages required but not available: 'glmnet', 'flexclust', 'faraway'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mcgibbsit.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘randtoolbox’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mcheatmaps.Rcheck/00install.out’ for details.
Packages required but not available: 'metafor', 'boot.heterogeneity'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Invalid NAMESPACE file, parsing gives:
Error in packageVersion("spdep"): there is no package called ‘spdep’

See section ‘Package namespaces’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mcll.Rcheck/00install.out’ for details.
Package required but not available: ‘memisc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'doParallel', 'doRNG'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mclustAddons.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘geometry’
checkRd: (7) MclustDRsubsel.Rd:33: \item in \describe must have non-empty label
checkRd: (7) MclustDRsubsel.Rd:34: \item in \describe must have non-empty label
checkRd: (7) MclustDRsubsel.Rd:41: \item in \describe must have non-empty label
checkRd: (7) MclustDRsubsel.Rd:42: \item in \describe must have non-empty label
checkRd: (7) MclustDRsubsel.Rd:43: \item in \describe must have non-empty label
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MCMC4Extremes.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘doParallel’
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mcmcderive)
  > 
  > test_check("mcmcderive")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 31 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-mcmc-derive.R:195:3): mcmc_derive in parallel ───────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'doParallel'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-mcmc-derive.R:195:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base withOneRestart(expr, restarts[[1L]])
   4.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 31 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘future.apply’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘orthopolynom’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MCMCglmm.Rcheck/00install.out’ for details.
Package required but not available: ‘MCMCglmm’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mcmcplots.Rcheck/00install.out’ for details.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘MCMCglmm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘readr’
Packages suggested but not available for checking:
  'spdep', 'maptools', 'survey'
Running ‘testthat.R’ [53s/79s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("mcmcsae")
  Loading required package: mcmcsae
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 336 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_modelmatrix.R:6:1): (code run outside of `test_that()`) ─────────
  <packageNotFoundError/error/condition>
  Error in `library(survey)`: there is no package called 'survey'
  Backtrace:
      ▆
   1. └─base::library(survey) at test_modelmatrix.R:6:0
  ── Error (test_prior_sampling.R:14:3): prior specification of regression component works ──
  <packageNotFoundError/error/condition>
  Error in `library(survey)`: there is no package called 'survey'
  Backtrace:
      ▆
   1. └─base::library(survey) at test_prior_sampling.R:14:2
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 336 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘area_level.Rmd’ using rmarkdown
--- finished re-building ‘area_level.Rmd’

--- re-building ‘linear_weighting.Rmd’ using rmarkdown
Quitting from lines 20-33 (linear_weighting.Rmd) 
Error: processing vignette ‘linear_weighting.Rmd’ failed with diagnostics:
there is no package called 'survey'
--- failed re-building ‘linear_weighting.Rmd’

--- re-building ‘unit_level.Rmd’ using rmarkdown
Quitting from lines 26-30 (unit_level.Rmd) 
Error: processing vignette ‘unit_level.Rmd’ failed with diagnostics:
there is no package called 'survey'
--- failed re-building ‘unit_level.Rmd’

SUMMARY: processing the following files failed:
  ‘linear_weighting.Rmd’ ‘unit_level.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘sn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'overlapping'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'survey', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ecr', 'vegan'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
do.linear.conjoint: no visible global function definition for
  ‘as.formula’
do.linear.conjoint: no visible global function definition for ‘lm’
do.linear.conjoint: no visible global function definition for
  ‘coefficients’
is.close.to.orthogonal: no visible global function definition for ‘cor’
mc.add.to.design: no visible global function definition for ‘combn’
mc.good.designs: no visible global function definition for ‘combn’
Undefined global functions or variables:
  as.formula coefficients combn cor lm
Consider adding
  importFrom("stats", "as.formula", "coefficients", "cor", "lm")
  importFrom("utils", "combn")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'multcomp', 'magic', 'MCMCpack'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'DoseFinding'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MCPModPack.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MCPMod.Rcheck/00install.out’ for details.
Packages required but not available: 'future.apply', 'rjags'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘multcomp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mcprofile.Rcheck/00install.out’ for details.
Package required but not available: ‘doParallel’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Checking should be performed on sources prepared by ‘R CMD build’.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘readr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘mctq.Rmd’ using rmarkdown
Quitting from lines 60-64 (mctq.Rmd) 
Error: processing vignette ‘mctq.Rmd’ failed with diagnostics:
there is no package called 'readr'
--- failed re-building ‘mctq.Rmd’

--- re-building ‘missing-sections.Rmd’ using rmarkdown
--- finished re-building ‘missing-sections.Rmd’

--- re-building ‘sjl-computation.Rmd’ using rmarkdown
--- finished re-building ‘sjl-computation.Rmd’

--- re-building ‘time-span-objects.Rmd’ using rmarkdown
--- finished re-building ‘time-span-objects.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'pcalg', 'mgm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'VIM', 'FactoMineR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘earth’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mda.Rcheck/00install.out’ for details.
Packages required but not available: 'orthopolynom', 'doParallel'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dendextend’
Running examples in ‘mdendro-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: linkage
> ### Title: Extended Agglomerative Hierarchical Clustering
> ### Aliases: linkage descplot
> ### Keywords: cluster
> 
> ### ** Examples
> 
> ## Plot and summary of unweighted arithmetic linkage (UPGMA) dendrogram
> lnk1 <- linkage(UScitiesD)
> plot(lnk1)
> summary(lnk1)
Call:
linkage(prox = UScitiesD,
        type.prox = "distance",
        digits = 0,
        method = "arithmetic",
        weighted = FALSE,
        group = "variable")

Binary dendrogram: TRUE

Descriptive measures:
      cor       sdr        ac        cc        tb 
0.8101937 0.6998814 0.7059747 0.3055556 0.9316262 
> 
> ## Linkage of similarity data (non-negative correlations)
> sim <- as.dist(cor(EuStockMarkets))
> lnk2 <- linkage(sim, type.prox = "similarity")
> plot(lnk2)
> 
> ## Use function as.dendrogram to plot with package dendextend
> d <- dist(scale(mtcars))  # distances of standardized data
> lnk <- linkage(d, digits = 1, method = "complete")
> lnk.dend <- as.dendrogram(lnk)
> plot(dendextend::set(lnk.dend, "branches_k_color", k = 4),
+      nodePar = list(cex = 0.4, lab.cex = 0.5))
Error in loadNamespace(x) : there is no package called ‘dendextend’
Calls: plot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mdendro-vignette.Rmd’ using rmarkdown
Quitting from lines 171-188 (mdendro-vignette.Rmd) 
Error: processing vignette ‘mdendro-vignette.Rmd’ failed with diagnostics:
there is no package called 'dendextend'
--- failed re-building ‘mdendro-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘psqn’

Package suggested but not available for checking: ‘catdata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mdhglm.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'RGtk2', 'coin'
'LazyData' is specified without a 'data' directory
Running examples in ‘mdir.logrank-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mdir.logrank
> ### Title: Two-sample multiple-direction log rank test
> ### Aliases: mdir.logrank
> 
> ### ** Examples
> 
> library(coin)
Error in library(coin) : there is no package called ‘coin’
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'RMySQL', 'leaflet', 'leaflet.extras', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'CDM', 'miceadds', 'sirt'

Packages which this enhances but not available for checking:
  'JointAI', 'jomo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'magic', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MDplot.Rcheck/00install.out’ for details.
Package required but not available: ‘linprog’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mdscore.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mdsdt.Rcheck/00install.out’ for details.
Package required but not available: ‘smacof’

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘RMySQL’

Packages suggested but not available for checking:
  'leaflet', 'etl', 'macleish', 'mosaic'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘dplR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dynlm', 'hdrcde'

Packages suggested but not available for checking:
  'car', 'ConvergenceConcepts', 'lmtest', 'strucchange', 'plm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'latentnet', 'vegan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'lmerTest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mederrRank.Rcheck/00install.out’ for details.
Package required but not available: ‘meteoland’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'multcomp', 'car'

Packages suggested but not available for checking:
  'arm', 'gam', 'glmnet', 'SuperLearner'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'doParallel', 'doRNG'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'doRNG'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'lme4'

Packages suggested but not available for checking: 'quantreg', 'speedglm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mediation', 'distr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
  'LazyDataCompression' is specified without a 'data' directory
Packages required but not available: 'rgdal', 'raster', 'rgeos', 'vegan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyverse', 'tm'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'seriation', 'TraMineR', 'WeightedCluster'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mefa4.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'vegan', 'mefa4'
Packages required but not available:
  'SKAT', 'pedgene', 'AnnotationDbi', 'GenomeInfoDb', 'RSQLite',
  'famSKATRC', 'kinship2'

Packages suggested but not available for checking:
  'TxDb.Hsapiens.UCSC.hg19.knownGene', 'org.Hs.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'doParallel', 'fpc', 'ggrepel', 'ggraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
.df: no visible global function definition for ‘logLik’
coef_simple: no visible global function definition for ‘coef’
fitall: no visible binding for global variable ‘as.formula’
fitbest: no visible binding for global variable ‘as.formula’
lmboot: no visible global function definition for ‘lm’
residuals.ensemble : <anonymous>: no visible global function definition
  for ‘resid’
residuals.ensemble : <anonymous>: no visible global function definition
  for ‘rstudent’
residuals.ensemble : <anonymous>: no visible global function definition
  for ‘fitted’
residuals.ensemble : <anonymous>: no visible global function definition
  for ‘influence.measures’
stdcoef: no visible global function definition for ‘coef’
stdcoef: no visible global function definition for ‘update’
summary.ensemble : <anonymous>: no visible global function definition
  for ‘logLik’
summary.ensemble : <anonymous>: no visible global function definition
  for ‘AIC’
summary.ensemble : <anonymous>: no visible global function definition
  for ‘fitted’
summary.resid_ensemble: no visible binding for global variable
  ‘rstudent’
summary.resid_ensemble: no visible global function definition for ‘sd’
summary.variable_ensemble: no visible global function definition for
  ‘sd’
Undefined global functions or variables:
  AIC as.formula coef fitted influence.measures lm logLik resid
  rstudent sd update
Consider adding
  importFrom("stats", "AIC", "as.formula", "coef", "fitted",
             "influence.measures", "lm", "logLik", "resid", "rstudent",
             "sd", "update")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘readr’
Running ‘testthat.R’ [6s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(meltr)
  > 
  > test_check("meltr")
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 114 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-melt-csv.R:70:3): nuls are dropped with a warning ───────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'readr'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(readr:::n_problems(x), 1) at test-melt-csv.R:70:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─base::loadNamespace(x)
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base withOneRestart(expr, restarts[[1L]])
   7.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 114 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘leaflet’

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

Packages suggested but not available for checking: 'haven', 'readODS'

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

Package suggested but not available for checking: ‘ggimage’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gdistance', 'raster', 'vegan'

Package suggested but not available for checking: ‘adegenet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'AER', 'car', 'lme4', 'haven'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/memisc.Rcheck/00install.out’ for details.
Packages required but not available: 'forecast', 'strucchange'

Package suggested but not available for checking: ‘xts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘README.Rmd’
Packages required but not available: 'viridis', 'HH'

Packages suggested but not available for checking:
  'devtools', 'rpart.plot', 'virtualPollen'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'quantreg', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Thresher', 'ClassDiscovery', 'dendextend', 'flexmix'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘mirt’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘randtoolbox’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'missForest', 'ggpubr', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arm', 'lme4', 'blme', 'broom.mixed'

Packages suggested but not available for checking:
  'future.apply', 'rstanarm', 'Amelia'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'geeM', 'ggformula', 'glmnet', 'kinship2'

Package suggested but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘INLA’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/meta4diag.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MetaAnalyser.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘GenABEL’
Malformed Description field: should contain one or more complete sentences.
dometa: no visible global function definition for ‘qchisq’
dometa: no visible global function definition for ‘median’
dometa: no visible global function definition for ‘pchisq’
forestplot: no visible global function definition for ‘pchisq’
forestplot: no visible global function definition for ‘qnorm’
forestplot: no visible global function definition for ‘points’
forestplot: no visible global function definition for ‘text’
metagwa.files: no visible global function definition for ‘read.csv’
metagwa.files: no visible global function definition for ‘write.csv’
metagwa.tables: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  median pchisq points qchisq qnorm read.csv text write.csv
Consider adding
  importFrom("graphics", "points", "text")
  importFrom("stats", "median", "pchisq", "qchisq", "qnorm")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘rstan’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MetabolAnalyze.Rcheck/00install.out’ for details.
Packages required but not available: 'ggimage', 'meta'

Package suggested but not available for checking: ‘downloadthis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'survminer', 'rms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/metabolighteR.Rcheck/00install.out’ for details.
Package required but not available: ‘enviPick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'C50', 'caret', 'mixOmics', 'pcaMethods', 'ropls'

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

Packages suggested but not available for checking:
  'lme4', 'M3C', 'future.apply', 'ggrepel', 'genuMet', 'ggstatsplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/metacart.Rcheck/00install.out’ for details.
Packages required but not available: 'factoextra', 'seqinr', 'Biostrings'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'taxize', 'seqinr', 'readr', 'vegan', 'GA'

Packages suggested but not available for checking: 'phyloseq', 'traits'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘vegan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'metafor', 'readr', 'rio'
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro-to-metaconfoundr.Rmd’ using rmarkdown
Quitting from lines 11-19 (intro-to-metaconfoundr.Rmd) 
Error: processing vignette ‘intro-to-metaconfoundr.Rmd’ failed with diagnostics:
there is no package called 'metafor'
--- failed re-building ‘intro-to-metaconfoundr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/metacor.Rcheck/00install.out’ for details.
Packages required but not available:
  'verification', 'spatstat.geom', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘cycHumanBloodData.csv’ ‘cycHumanBloodDesign.csv’
  ‘cycMouseLiverProtein.txt’ ‘cycMouseLiverRNA.csv’ ‘cycSimu4h2d.csv’
  ‘cycYeastCycle.csv’ ‘example’
Packages suggested but not available for checking:
  'metafor', 'lme4', 'meta', 'netmeta', 'rms'
Packages required but not available:
  'SPARQL', 'rcdk', 'RSQLite', 'gsubfn', 'WikidataQueryServiceR',
  'R.utils', 'KEGGREST', 'Hmisc', 'Rdisop'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/metadynminer3d.Rcheck/00install.out’ for details.
Package required but not available: ‘caret’

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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

Package suggested but not available for checking: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'lme4', 'Epi', 'glmmTMB', 'multcomp', 'R.rsp', 'wildmeta'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/metafor.Rcheck/00install.out’ for details.
Package required but not available: ‘glmnet’

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

Package suggested but not available for checking: ‘devtools’

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

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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
Packages required but not available:
  'multtest', 'Rmisc', 'Biobase', 'RMySQL', 'GEOquery', 'GEOmetadb',
  'RSQLite', 'ggpubr', 'manhattanly', 'AnnotationDbi', 'readr',
  'plotly'

Package suggested but not available for checking: ‘snplist’

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

Suggests orphaned package: ‘udunits2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'maptools', 'rgeos', 'rgrass7', 'raster', 'spatstat.geom',
  'spatstat.random'

Package suggested but not available for checking: ‘rasterVis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'doParallel', 'metagenomeSeq', 'DESeq2', 'edgeR'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'GEOquery', 'org.Hs.eg.db', 'VennDiagram', 'annaffy',
  'hgu133plus2.db', 'hgu133a.db', 'hgu95av2.db'
Packages required but not available: 'Hmisc', 'metafor'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'gamlss', 'meta', 'lme4', 'lmerTest', 'zCompositions'

Packages suggested but not available for checking: 'repmis', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'metafor', 'lme4'

Packages suggested but not available for checking: 'rjags', 'ggmcmc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'GGally', 'ggforce', 'ggrepel', 'lme4', 'lmerTest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Biobase', 'GSEABase', 'genefilter'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘metafor’
Package vignette with placeholder title ‘Vignette Title’:
  ‘how_to_use_crosshairs.Rmd’
Error(s) in re-building vignettes:
  ...
--- re-building ‘how_to_use_crosshairs.Rmd’ using rmarkdown
Quitting from lines 128-163 (how_to_use_crosshairs.Rmd) 
Error: processing vignette ‘how_to_use_crosshairs.Rmd’ failed with diagnostics:
there is no package called 'metafor'
--- failed re-building ‘how_to_use_crosshairs.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'metafor', 'fastGHQuad', 'lme4', 'Rfast', 'doParallel', 'doRNG'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘grImport’
Running ‘mpost.R’ [1s/1s]
  Running ‘path.R’ [0s/1s]
Running the tests in ‘tests/mpost.R’ failed.
Complete output:
  > 
  > library(metapost)
  
  Attaching package: 'metapost'
  
  The following object is masked from 'package:stats':
  
      cycle
  
  The following object is masked from 'package:base':
  
      dir
  
  > library(grid)
  > p <- knot(0, 0) + dir(45) + dir(0:9*-10) + knot(unit(6, "cm"), 0)
  > metapost(p, "fig.mp")
  > mpost("fig.mp", tracing=TRUE)
  This is MetaPost, version 2.01 (TeX Live 2022/dev/Debian) (kpathsea version 6.3.4/dev)
  (/usr/share/texlive/texmf-dist/metapost/base/mpost.mp
  (/usr/share/texlive/texmf-dist/metapost/base/plain.mp
  Preloading the plain mem file, version 1.005) ) (./fig.mp [1] )
  (see the transcript file for additional information)
  1 output file written: fig.1
  Transcript written on fig.log.
  > 
  > controls <- mptrace("fig.log")
  Read 8 items
  Read 8 items
  Read 8 items
  Read 8 items
  Read 8 items
  Read 8 items
  Read 8 items
  Read 8 items
  Read 8 items
  Read 8 items
  > 
  > library(grImport)
  Error in library(grImport) : there is no package called 'grImport'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'TFisher', 'mutoss'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dendextend', 'ggforce', 'ggrepel', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'metafor', 'lme4'

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

Packages suggested but not available for checking: 'metafor', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstpm2', 'meta', 'survRM2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'DESeq2', 'VennDiagram'
Error(s) in re-building vignettes:
  ...
--- re-building ‘metaRNASeq.Rnw’ using Sweave
Error: processing vignette ‘metaRNASeq.Rnw’ failed with diagnostics:
Running ‘texi2dvi’ on ‘metaRNASeq.tex’ failed.
LaTeX errors:
! Package pdftex.def Error: File `venn_jpeg.jpg' not found: using draft setting
.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Emergency stop.
 ...                                              
                                                  
l.432 ...ics[width = .85\textwidth]{venn_jpeg.jpg}
                                                  
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘metaRNASeq.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘maxLik’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'metafor', 'semPlot', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/metaSEM.Rcheck/00install.out’ for details.
Package required but not available: ‘meta’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'forestplot', 'metafor'

Package suggested but not available for checking: ‘shinystan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘haven’
Running examples in ‘metatools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_variables
> ### Title: Add Missing Variables
> ### Aliases: add_variables
> 
> ### ** Examples
> 
> library(metacore)
> library(haven)
Error in library(haven) : there is no package called ‘haven’
Execution halted
Package required but not available: ‘lme4’

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

Packages suggested but not available for checking: 'epiR', 'metafor'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘metaSEM’
Packages required but not available: 'nullabor', 'metafor', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'metafor', 'forestmodel'

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

Packages suggested but not available for checking: 'rgdal', 'rasterVis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/meteogRam.Rcheck/00install.out’ for details.
Packages required but not available: 'spdep', 'rgdal'

Packages suggested but not available for checking:
  'forecast', 'spacetime', 'stars'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spacetime', 'rgdal', 'gstat', 'raster', 'snowfall'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggforce’
Error(s) in re-building vignettes:
  ...
--- re-building ‘aemet.Rmd’ using rmarkdown
Quitting from lines 23-28 (aemet.Rmd) 
Error: processing vignette ‘aemet.Rmd’ failed with diagnostics:
there is no package called 'ggforce'
--- failed re-building ‘aemet.Rmd’

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

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

--- re-building ‘meteocat.Rmd’ using rmarkdown
Quitting from lines 23-29 (meteocat.Rmd) 
Error: processing vignette ‘meteocat.Rmd’ failed with diagnostics:
there is no package called 'ggforce'
--- failed re-building ‘meteocat.Rmd’

--- re-building ‘meteoclimatic.Rmd’ using rmarkdown
Quitting from lines 23-27 (meteoclimatic.Rmd) 
Error: processing vignette ‘meteoclimatic.Rmd’ failed with diagnostics:
there is no package called 'ggforce'
--- failed re-building ‘meteoclimatic.Rmd’

--- re-building ‘meteogalicia.Rmd’ using rmarkdown
Quitting from lines 23-27 (meteogalicia.Rmd) 
Error: processing vignette ‘meteogalicia.Rmd’ failed with diagnostics:
there is no package called 'ggforce'
--- failed re-building ‘meteogalicia.Rmd’

--- re-building ‘ria.Rmd’ using rmarkdown
Quitting from lines 23-27 (ria.Rmd) 
Error: processing vignette ‘ria.Rmd’ failed with diagnostics:
there is no package called 'ggforce'
--- failed re-building ‘ria.Rmd’

SUMMARY: processing the following files failed:
  ‘aemet.Rmd’ ‘meteocat.Rmd’ ‘meteoclimatic.Rmd’ ‘meteogalicia.Rmd’
  ‘ria.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘distr’

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

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

Package suggested but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MethodCompare.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
getdata: no visible global function definition for ‘read.csv’
plotdata: no visible global function definition for ‘head’
Undefined global functions or variables:
  head read.csv
Consider adding
  importFrom("utils", "head", "read.csv")
to your NAMESPACE file.
RUVRand: no visible global function definition for ‘barplot’
RUVRand: no visible global function definition for ‘prcomp’
RuvRandIter: no visible global function definition for ‘kmeans’
RuvRandIter: no visible global function definition for ‘barplot’
RuvRandIter: no visible global function definition for ‘prcomp’
opt: no visible global function definition for ‘optim’
printdata: no visible global function definition for ‘head’
Undefined global functions or variables:
  barplot head kmeans optim prcomp
Consider adding
  importFrom("graphics", "barplot")
  importFrom("stats", "kmeans", "optim", "prcomp")
  importFrom("utils", "head")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
checkRd: (7) Ra.Rd:33-39: \item in \describe must have non-empty label
checkRd: (7) Rn.Rd:58-59: \item in \describe must have non-empty label
checkRd: (7) Rn.Rd:60: \item in \describe must have non-empty label
checkRd: (7) Rn.Rd:61: \item in \describe must have non-empty label
checkRd: (7) Rns.Rd:22: \item in \describe must have non-empty label
checkRd: (7) Rso.Rd:34-41: \item in \describe must have non-empty label
checkRd: (7) Rso.Rd:42: \item in \describe must have non-empty label
checkRd: (7) estG.Rd:44-45: \item in \describe must have non-empty label
checkRd: (7) estG.Rd:46-53: \item in \describe must have non-empty label
checkRd: (7) estG.Rd:54-59: \item in \describe must have non-empty label
checkRd: (7) estP.Rd:23: \item in \describe must have non-empty label
checkRd: (7) estP.Rd:24: \item in \describe must have non-empty label
checkRd: (7) estP.Rd:25: \item in \describe must have non-empty label
checkRd: (7) estP.Rd:26: \item in \describe must have non-empty label
checkRd: (7) estP.Rd:27: \item in \describe must have non-empty label
checkRd: (7) estRs.Rd:32: \item in \describe must have non-empty label
checkRd: (7) estRs.Rd:33: \item in \describe must have non-empty label
checkRd: (7) w.Rd:21-27: \item in \describe must have non-empty label
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MetProc_output.pdf’ ‘sample_removed.csv’ ‘sample_retained.csv’
Package required but not available: ‘vegan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/metropolis.Rcheck/00install.out’ for details.
Package required but not available: ‘fields’

Packages suggested but not available for checking:
  'maptools', 'irlba', 'viridis', 'raster', 'rgdal'

Suggests orphaned package: ‘udunits2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'MetabolAnalyze', 'Rfast', 'vroom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'timereg', 'lava'

Packages suggested but not available for checking:
  'prodlim', 'cmprsk', 'icenReg'

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

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

Packages suggested but not available for checking:
  'cobs', 'gmm', 'ismev', 'TruncatedNormal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rstpm2’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mexhaz.Rcheck/00install.out’ for details.
Package required but not available: ‘qusage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Packages required but not available: 'duckdb', 'RPostgres', 'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'betapart', 'dendextend', 'FactoMineR', 'gawdis', 'geometry',
  'ggrepel', 'Hmisc', 'rstatix', 'vegan'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'tseries', 'tsDyn', 'forecast'
Package required but not available: ‘dtw’

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'funData', 'irlba'

Package suggested but not available for checking: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mfp.Rcheck/00install.out’ for details.
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.
Packages required but not available: 'Ball', 'dr', 'doParallel'

Packages suggested but not available for checking:
  'randomForestSRC', 'SIS', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lmtest', 'betareg'

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

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dataRetrieval’
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'qgam', 'gamm4', 'viridis', 'GGally'

Package suggested but not available for checking: ‘webshot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mgcv.Rcheck/00install.out’ for details.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Package required but not available: ‘R.utils’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'Hmisc', 'qgraph'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Biobase', 'ismev'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'leaflet', 'spgwr', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MHadaptive.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘MCMCpack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mhsmm.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mhtboot.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘structSSI’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'truncreg', 'maxLik'

Package suggested but not available for checking: ‘lmtest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘imp4p’

Packages suggested but not available for checking: 'Biobase', 'R.rsp'

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

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/micar.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'BIFIEsurvey', 'blme', 'car', 'CDM', 'lme4', 'MBESS', 'MCMCglmm',
  'mdmb', 'sirt', 'synthpop', 'TAM'

Packages which this enhances but not available for checking:
  'Amelia', 'jomo', 'micemd', 'mitml'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/miceadds.Rcheck/00install.out’ for details.
Packages required but not available: 'rms', 'mitml', 'car'

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lmtest', 'micEcon', 'systemfit'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'systemfit', 'micEcon'

Packages suggested but not available for checking: 'maxLik', 'AER'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'Ecdat', 'micEcon'
Running examples in ‘micEconIndex-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: priceIndex
> ### Title: Calculate Price Indices
> ### Aliases: priceIndex
> ### Keywords: models
> 
> ### ** Examples
> 
>    data( Missong03E7.7, package = "micEcon" )
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘micEcon’
Calls: data -> find.package
Execution halted
Running ‘indices.R’ [0s/1s]
Running the tests in ‘tests/indices.R’ failed.
Complete output:
  > library( "micEconIndex" )
  > options( digits = 4 )
  > 
  > ## function for printIndexing indices
  > printIndices <- function( what, ... ) {
  +    for( i in c( "Laspeyres", "Paasche", "Fisher" ) ) {
  +       cat( "\n", i, "\n" )
  +       if( what == "p" ) {
  +          index <- priceIndex( ..., method = i, weights = TRUE )
  +       } else {
  +          index <- quantityIndex( ..., method = i, weights = TRUE )
  +       }
  +       print( index )
  +       testRowSums <- rowSums( attributes( index )$weights[ !is.na( index ), ] )
  +       names( testRowSums ) <- NULL
  +       if( all.equal( testRowSums,
  +          rep( 1, sum( !is.na( index ) ) ) ) != TRUE ) {
  +          cat( "\nrowSums are not equal to one!!!\n\n" )
  +       }
  +    }
  + }
  > 
  > ## Missong03E7.7
  > data( Missong03E7.7, package = "micEcon" )
  Error in find.package(package, lib.loc, verbose = verbose) : 
    there is no package called 'micEcon'
  Calls: data -> find.package
  Execution halted
Package required but not available: ‘plm’

Packages suggested but not available for checking: 'Ecdat', 'systemfit'

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

Package suggested but not available for checking: ‘micEcon’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'jomo'

Package suggested but not available for checking: ‘VIM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggpubr', 'DescTools'

Package suggested but not available for checking: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'broom.mixed', 'glmnet', 'haven', 'lme4', 'lmtest', 'metafor',
  'mitml', 'miceadds'
Running examples in ‘mice-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: D1
> ### Title: Compare two nested models using D1-statistic
> ### Aliases: D1
> 
> ### ** Examples
> 
> # Compare two linear models:
> imp <- mice(nhanes2, seed = 51009, print = FALSE)
> mi1 <- with(data = imp, expr = lm(bmi ~ age + hyp + chl))
> mi0 <- with(data = imp, expr = lm(bmi ~ age + hyp))
> D1(mi1, mi0)
Error in loadNamespace(x) : there is no package called ‘mitml’
Calls: D1 ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'doBy', 'flexclust', 'irr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'biotools', 'MVN', 'deseasonalize', 'devtools'
Running examples in ‘micompr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: assumptions.cmpoutput
> ### Title: Get assumptions for parametric tests performed on output
> ###   comparisons
> ### Aliases: assumptions.cmpoutput
> 
> ### ** Examples
> 
> 
> # Create a cmpoutput object from the provided datasets
> cmp <- cmpoutput("All", 0.9, pphpc_ok$data[["All"]], pphpc_ok$obs_lvls)
> 
> # Get the assumptions for the parametric tests performed in cmp
> acmp <- assumptions(cmp)
MANOVA assumptions require 'MVN' and 'biotools' packages.
Error in `*tmp*`[[i]] : subscript out of bounds
Calls: assumptions -> assumptions.cmpoutput
Execution halted
Running ‘testthat.R’ [12s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Copyright (c) 2016 Nuno Fachada
  > # Distributed under the MIT License (http://opensource.org/licenses/MIT)
  > 
  > library(testthat)
  > 
  > test_check("micompr")
  Loading required package: micompr
  [ FAIL 2 | WARN 67 | SKIP 0 | PASS 291 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_cmpoutput.R:214:3): assumptions.cmpoutput creates the correct object ──
  <subscriptOutOfBoundsError/error/condition>
  Error in ``*tmp*`[[i]]`: subscript out of bounds
  Backtrace:
      ▆
   1. ├─micompr::assumptions(cmp) at test_cmpoutput.R:214:2
   2. └─micompr:::assumptions.cmpoutput(cmp)
  ── Error (test_micomp.R:281:3): micomp assumptions have the correct properties ──
  <subscriptOutOfBoundsError/error/condition>
  Error in ``*tmp*`[[i]]`: subscript out of bounds
  Backtrace:
      ▆
   1. ├─micompr::assumptions(mic1a) at test_micomp.R:281:2
   2. └─micompr:::assumptions.micomp(mic1a)
   3.   └─base::lapply(obj, function(x) assumptions(x))
   4.     └─micompr FUN(X[[i]], ...)
   5.       ├─micompr::assumptions(x)
   6.       └─micompr:::assumptions.cmpoutput(x)
  
  [ FAIL 2 | WARN 67 | SKIP 0 | PASS 291 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘paper.Rnw’ using knitr
Warning in wilcox.test.default(x = DATA[[1L]], y = DATA[[2L]], ...) :
  cannot compute exact p-value with ties
Quitting from lines 341-342 (paper.Rnw) 
Error: processing vignette ‘paper.Rnw’ failed with diagnostics:
subscript out of bounds
--- failed re-building ‘paper.Rnw’

--- re-building ‘tolatex-examples.Rnw’ using knitr
Warning in wilcox.test.default(x = DATA[[1L]], y = DATA[[2L]], ...) :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = DATA[[1L]], y = DATA[[2L]], ...) :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = DATA[[1L]], y = DATA[[2L]], ...) :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = DATA[[1L]], y = DATA[[2L]], ...) :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = DATA[[1L]], y = DATA[[2L]], ...) :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = DATA[[1L]], y = DATA[[2L]], ...) :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = DATA[[1L]], y = DATA[[2L]], ...) :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = DATA[[1L]], y = DATA[[2L]], ...) :
  cannot compute exact p-value with ties
--- finished re-building ‘tolatex-examples.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘distr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘multcomp’
Packages required but not available:
  'phyloseq', 'vegan', 'ggpubr', 'DESeq2', 'SummarizedExperiment',
  'S4Vectors', 'rstatix', 'phangorn', 'edgeR'

Packages suggested but not available for checking:
  'dada2', 'Biostrings', 'DECIPHER'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggrepel', 'lmerTest', 'modeest', 'phyloseq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'microseq', 'microcontax'

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

Package suggested but not available for checking: ‘microcontax.data’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘vegan’

Packages suggested but not available for checking:
  'GUniFrac', 'ggpubr', 'ggrepel', 'agricolae', 'picante'

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
Packages required but not available: 'maptools', 'rgdal'

Package suggested but not available for checking: ‘rgeos’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Package suggested but not available for checking: ‘readr’
Running ‘testthat.R’ [8s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(MicroMoB)
  > 
  > test_check("MicroMoB")
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 882 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-api_mosquitoes_plumber.R:19:3): API is alive ──────────────────
  api$is_alive() is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Error (test-api_mosquitoes_plumber.R:24:3): endpoints error properly ────────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Failed to connect to localhost port 5741 after 0 ms: Connection refused
  Backtrace:
      ▆
   1. └─httr::GET(root_path, port = api_port, path = "config_global_parameters") at test-api_mosquitoes_plumber.R:24:2
   2.   └─httr:::request_perform(req, hu$handle$handle)
   3.     ├─httr:::request_fetch(req$output, req$url, handle)
   4.     └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   5.       └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test-api_mosquitoes_plumber.R:144:3): run simulation via API ─────────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Failed to connect to localhost port 5741 after 0 ms: Connection refused
  Backtrace:
      ▆
   1. └─httr::GET(...) at test-api_mosquitoes_plumber.R:144:2
   2.   └─httr:::request_perform(req, hu$handle$handle)
   3.     ├─httr:::request_fetch(req$output, req$url, handle)
   4.     └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   5.       └─curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 882 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MicroNiche.Rcheck/00install.out’ for details.
Package required but not available: ‘microseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'HH'

Package suggested but not available for checking: ‘latticeExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/microPop.Rcheck/00install.out’ for details.
Packages required but not available: 'devtools', 'readr'

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/microseq.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘httptest’
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(microservices)
  > test_check("microservices")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 12 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-endpoint-plumber-{route_name}.R:13:1): (code run outside of `test_that()`) ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'httptest'
  Backtrace:
      ▆
   1. ├─microservices:::test_http(...) at test-endpoint-plumber-{route_name}.R:13:0
   2. └─base::loadNamespace(x) at tests/testthat/helpers-xyz.R:5:8
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base withOneRestart(expr, restarts[[1L]])
   5.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 12 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/microsimulation.Rcheck/00install.out’ for details.
Packages required but not available: 'AzureAuth', 'AzureGraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'future.apply', 'ggside'

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

Package suggested but not available for checking: ‘xlsx’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'genefilter', 'SQN'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'MCMCpack', 'R2jags'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doRNG', 'doParallel', 'randtoolbox'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'quantreg', 'forecast'

Package suggested but not available for checking: ‘xts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MIDN.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘migration.indices’

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggforce', 'ggraph', 'furrr', 'sna'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gWidgets2', 'mi', 'arm'

Package suggested but not available for checking: ‘gWidgets2RGtk2’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'R2jags', 'matlib'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'glmnet'

Packages suggested but not available for checking:
  'doFuture', 'future.apply'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
nat_hist: no visible global function definition for ‘data’
nat_hist: no visible binding for global variable ‘current.other’
t_mal: no visible global function definition for ‘uniroot’
t_prog: no visible global function definition for ‘rlnorm’
tdeath_lung: no visible global function definition for ‘data’
tdeath_lung: no visible binding for global variable ‘ci.lung’
tdeath_lung: no visible binding for global variable ‘current.other’
tdeath_lung: no visible binding for global variable ‘former.other’
tdeath_lung: no visible binding for global variable ‘never.other’
tdeath_other: no visible global function definition for ‘data’
tdeath_other: no visible binding for global variable ‘ci.lung’
tdeath_other: no visible binding for global variable ‘current.other’
tdeath_other: no visible binding for global variable ‘former.other’
tdeath_other: no visible binding for global variable ‘never.other’
Undefined global functions or variables:
  ci.lung current.other data former.other never.other rlnorm uniroot
Consider adding
  importFrom("stats", "rlnorm", "uniroot")
  importFrom("utils", "data")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/miLineage.Rcheck/00install.out’ for details.
Package required but not available: ‘gaston’

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

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'glmnet', 'softImpute', 'FactoMineR', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'glmnet', 'heatmaply', 'plotly', 'survminer'

Package suggested but not available for checking: ‘ggfortify’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
MImix.default: no visible binding for global variable ‘coef’
MImix.default: no visible binding for global variable ‘vcov’
MImix.one: no visible global function definition for ‘qnorm’
MImix.one: no visible global function definition for ‘uniroot’
mixcdf.target: no visible global function definition for ‘pnorm’
print.MImixresult: no visible global function definition for ‘coef’
print.MImixresult: no visible global function definition for ‘vcov’
summary.MImixresult: no visible global function definition for ‘coef’
summary.MImixresult: no visible global function definition for ‘vcov’
summary.MImixresult: no visible global function definition for ‘qt’
Undefined global functions or variables:
  coef pnorm qnorm qt uniroot vcov
Consider adding
  importFrom("stats", "coef", "pnorm", "qnorm", "qt", "uniroot", "vcov")
to your NAMESPACE file.
Rd file 'MImix.Rd':
  \usage lines wider than 90 characters:
     MImix(results,variances,weights = 1/length(results), percentiles = c(0.025, 0.5, 0.975), ...) 

These lines will be truncated in the PDF manual.
Packages required but not available: 'readr', 'R.utils', 'xts', 'dygraphs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'raster', 'rgdal', 'maxnet', 'dismo', 'ecospat', 'latticeExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'JWileymisc', 'tm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MinEDfind.Rcheck/00install.out’ for details.
miney : plot.initial.matrix: no visible global function definition for
  ‘rect’
miney : plot.known.matrix: no visible global function definition for
  ‘rect’
miney : plot.known.matrix: no visible global function definition for
  ‘text’
miney: no visible global function definition for ‘locator’
miney: no visible global function definition for ‘rect’
miney: no visible global function definition for ‘title’
Undefined global functions or variables:
  locator rect text title
Consider adding
  importFrom("graphics", "locator", "rect", "text", "title")
to your NAMESPACE file.
Packages suggested but not available for checking: 'devtools', 'testthis'
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'randtoolbox', 'MaxPro', 'doParallel', 'doSNOW', 'DoE.base', 'FrF2',
  'geometry'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'meta', 'metafor'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'seqinr', 'Biostrings'
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(minSNPs)
  The minSNPs version loaded is: 0.0.2
  > library(Biostrings)
  Error in library(Biostrings) : there is no package called 'Biostrings'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MinSNPs_Workflow.Rmd’ using rmarkdown
Quitting from lines 18-21 (MinSNPs_Workflow.Rmd) 
Error: processing vignette ‘MinSNPs_Workflow.Rmd’ failed with diagnostics:
there is no package called 'Biostrings'
--- failed re-building ‘MinSNPs_Workflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MInt.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘sybil’
'LazyData' is specified without a 'data' directory
Running examples in ‘minval-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: characterizeReactions
> ### Title: Characterize stoichiometric reactions by compartments and
> ###   reaction type
> ### Aliases: characterizeReactions
> 
> ### ** Examples
> 
> # Loading a set of stoichiometric reactions
> glycolysis <- read.csv(system.file("extdata/glycolysisModel.csv",package = "minval"), sep='\t')
> 
> # Characterizing the reactions
> characterizeReactions(reactionList = glycolysis$REACTION)
Error in is.null(right) || is.na(right) : 
  'length = 2' in coercion to 'logical(1)'
Calls: characterizeReactions -> validateSyntax -> unlist -> lapply -> FUN
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MINVALintroduction.Rmd’ using rmarkdown
Quitting from lines 21-25 (MINVALintroduction.Rmd) 
Error: processing vignette ‘MINVALintroduction.Rmd’ failed with diagnostics:
there is no package called 'sybil'
--- failed re-building ‘MINVALintroduction.Rmd’

--- re-building ‘characterizeReactions.Rmd’ using rmarkdown
Quitting from lines 45-47 (characterizeReactions.Rmd) 
Error: processing vignette ‘characterizeReactions.Rmd’ failed with diagnostics:
'length = 3' in coercion to 'logical(1)'
--- failed re-building ‘characterizeReactions.Rmd’

SUMMARY: processing the following files failed:
  ‘MINVALintroduction.Rmd’ ‘characterizeReactions.Rmd’

Error: Vignette re-building failed.
Execution halted
minxent.multiple: no visible global function definition for ‘cov.wt’
minxent.single: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  cov.wt optimize
Consider adding
  importFrom("stats", "cov.wt", "optimize")
to your NAMESPACE file.
Rd file 'minxent.multiple.Rd':
  \examples lines wider than 100 characters:
     minxent.multiple(q=q,G=G,eta=eta,c(0,0)) #estimates of lagrangian multipliers and MinxEnt distribution

Rd file 'minxent.single.Rd':
  \examples lines wider than 100 characters:
     minxent.single(q=q,G=G,eta=eta,c(0)) # estimate of lagrangian multipliers and Kullback minimimum cross entropy distribution

These lines will be truncated in the PDF manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mipfp.Rcheck/00install.out’ for details.
Package required but not available: ‘doBy’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'showtext'

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
.FCLoess: no visible global function definition for ‘loess’
.FCLoessM: no visible global function definition for ‘loess’
.FCLoessM: no visible global function definition for ‘median’
.Import.Luminex: no visible global function definition for ‘read.csv’
.Intra.Me: no visible global function definition for ‘sd’
.Intra.Me: no visible global function definition for ‘quantile’
.Intra.Me: no visible global function definition for ‘qchisq’
.Intra.Median: no visible global function definition for ‘median’
.boxplot.rtprofile: no visible global function definition for ‘boxplot’
.denplot: no visible global function definition for ‘density’
.denplot: no visible global function definition for ‘abline’
.normalize.Luminex: no visible global function definition for ‘sd’
.normalize.qrtpcr: no visible global function definition for ‘density’
.validate.default: no visible global function definition for ‘t.test’
Undefined global functions or variables:
  abline boxplot density loess median qchisq quantile read.csv sd
  t.test
Consider adding
  importFrom("graphics", "abline", "boxplot")
  importFrom("stats", "density", "loess", "median", "qchisq", "quantile",
             "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Package required but not available: ‘arm’

Packages suggested but not available for checking: 'betareg', 'sn'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plotly', 'readr', 'topicmodels', 'wordcloud'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'quantreg', 'GUniFrac', 'lme4', 'mixtools'

Packages suggested but not available for checking: 'vegan', 'tidyverse'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'globaltest', 'GlobalAncova', 'RepeatedHighDim'

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

Packages suggested but not available for checking:
  'latticeExtra', 'sirt', 'plink', 'mirtCAT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'R2jags', 'MCMCpack'

Package suggested but not available for checking: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/miscFuncs.Rcheck/00install.out’ for details.
Package required but not available: ‘mlogit’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Ecdat’
Running examples in ‘miscTools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: colMedians
> ### Title: Medians of Columns
> ### Aliases: colMedians
> ### Keywords: array
> 
> ### ** Examples
> 
>    data( "Electricity", package = "Ecdat" )
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘Ecdat’
Calls: data -> find.package
Execution halted
Running ‘colMediansTest.R’ [0s/1s]
  Running ‘ddnormTest.R’ [0s/1s]
  Comparing ‘ddnormTest.Rout’ to ‘ddnormTest.Rout.save’ ... OK
  Running ‘insertColRow.R’ [0s/1s]
  Comparing ‘insertColRow.Rout’ to ‘insertColRow.Rout.save’ ... OK
  Running ‘lmMethods.R’ [0s/1s]
  Comparing ‘lmMethods.Rout’ to ‘lmMethods.Rout.save’ ... OK
  Running ‘margEffTest.R’ [0s/1s]
  Comparing ‘margEffTest.Rout’ to ‘margEffTest.Rout.save’ ... OK
  Running ‘semidefTest.R’ [0s/1s]
  Comparing ‘semidefTest.Rout’ to ‘semidefTest.Rout.save’ ... OK
  Running ‘stdErTests.R’ [0s/1s]
  Comparing ‘stdErTests.Rout’ to ‘stdErTests.Rout.save’ ... OK
  Running ‘sumKeepAttrTest.R’ [0s/1s]
  Comparing ‘sumKeepAttrTest.Rout’ to ‘sumKeepAttrTest.Rout.save’ ... OK
  Running ‘summarizeDF_tests.R’ [0s/1s]
  Comparing ‘summarizeDF_tests.Rout’ to ‘summarizeDF_tests.Rout.save’ ... OK
Running the tests in ‘tests/colMediansTest.R’ failed.
Complete output:
  > library( "miscTools" )
  > 
  > 
  > ## matrix
  > m <- matrix( 1:24, nrow = 6, ncol = 4 )
  > 
  > cm1 <- colMedians( m )
  > print( cm1 )
  [1]  3.5  9.5 15.5 21.5
  > 
  > rm1 <- rowMedians( m )
  > print( rm1 )
  [1] 10 11 12 13 14 15
  > 
  > all.equal( cm1, rowMedians( t( m ) ) )
  [1] TRUE
  > all.equal( rm1, colMedians( t( m ) ) )
  [1] TRUE
  > 
  > 
  > ## data.frame
  > data( "Electricity", package = "Ecdat" )
  Error in find.package(package, lib.loc, verbose = verbose) : 
    there is no package called 'Ecdat'
  Calls: data -> find.package
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'forrel', 'pedtools', 'plotly', 'highcharter', 'tidyverse',
  'DirichletReg'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'vegan', 'aSPU'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mixtools', 'tseries'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Amelia', 'Hmisc', 'ltm', 'mi', 'missForest', 'missMDA',
  'pcaMethods', 'VIM'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rms', 'relsurv', 'cmprsk'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘sbw’
Packages required but not available: 'itertools', 'doRNG'

Package suggested but not available for checking: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'mcmcplots', 'ggpubr', 'ggmcmc', 'BCEA', 'R2jags'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'FactoMineR', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'future.apply', 'sbm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'car', 'tseries', 'DoE.base', 'FrF2', 'DiceEval', 'DiceView',
  'fdapace'
Running examples in ‘mistat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: LATHYPPISTON
> ### Title: Latin Hypercube Design for the Piston Simulator
> ### Aliases: LATHYPPISTON
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(LATHYPPISTON)
> 
> library(DiceEval)
Error in library(DiceEval) : there is no package called ‘DiceEval’
Execution halted
Package required but not available: ‘doParallel’

Package suggested but not available for checking: ‘KrigInv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MiST.Rcheck/00install.out’ for details.
Packages required but not available: 'haven', 'lme4', 'r2mlm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'jomo', 'haven'

Packages suggested but not available for checking:
  'miceadds', 'Amelia', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Biostrings', 'ComplexHeatmap', 'GenomicRanges', 'IRanges',
  'mcclust', 'Rsamtools'

Packages suggested but not available for checking:
  'clustree', 'gam', 'karyoploteR', 'plotly', 'regioneR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'condMVNorm', 'Hmisc', 'MCMCpack', 'tmvtnorm'

Package suggested but not available for checking: ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'fastGHQuad'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fGarch', 'MCMCpack'

Package suggested but not available for checking: ‘fma’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mixcat.Rcheck/00install.out’ for details.
Package required but not available: ‘tmvtnorm’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'expm', 'kdensity'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'flexsurv', 'survey', 'gam', 'timereg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mcclust’
Packages required but not available: 'fMultivar', 'irlba', 'chebpol'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gaussquad', 'Rmpfr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'brglm', 'lme4'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MixedTS.Rcheck/00install.out’ for details.
Package required but not available: ‘daewr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'MixSim', 'EMCluster'

Package which this enhances but not available for checking: ‘AnalyzeFMRI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Bessel', 'ghyp', 'mixture'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mixOmics', 'vegan', 'phyloseq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'multcomp'

Package suggested but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'maxLik', 'randtoolbox', 'readr'

Package suggested but not available for checking: ‘mlogit’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'metafor', 'meta', 'dosresmeta'
Running examples in ‘mixmeta-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: alcohol
> ### Title: Alcohol Intake and Colorectal Cancer
> ### Aliases: alcohol
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ### REPRODUCE THE RESULTS IN CRIPPA ET AL (2016) AND ORSINI ET AL (2012)
> 
> # LOAD THE PACKAGE dosresmeta AND splines
> library(dosresmeta) ; library(splines)
Error in library(dosresmeta) : there is no package called ‘dosresmeta’
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MixOptim.Rcheck/00install.out’ for details.
Packages required but not available:
  'Rfast', 'gamlss.dist', 'lmtest', 'ggrepel', 'gamlss'

Packages suggested but not available for checking: 'devtools', 'ggfortify'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MixSAL.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mixsep.Rcheck/00install.out’ for details.
Packages required but not available:
  'R2jags', 'MCMCpack', 'ggmcmc', 'splancs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MixSim.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mixsmsn.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘irlba’

Package suggested but not available for checking: ‘REBayes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
fit.mixtNB: no visible global function definition for ‘dnbinom’
fit.mixtNB: no visible global function definition for ‘nlminb’
wald.test: no visible global function definition for ‘pnorm’
wald.test: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  dnbinom nlminb p.adjust pnorm
Consider adding
  importFrom("stats", "dnbinom", "nlminb", "p.adjust", "pnorm")
to your NAMESPACE file.
Package required but not available: ‘segmented’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mixture.Rcheck/00install.out’ for details.
Packages required but not available: 'alabama', 'ashr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggrepel', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘doParallel’
Package suggested but not available for checking: ‘Amelia’
Running examples in ‘MKinfer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mi.t.test
> ### Title: Multiple Imputation Student's t-Test
> ### Aliases: mi.t.test mi.t.test.default
> ### Keywords: htest
> 
> ### ** Examples
> 
> ## Generate some data
> set.seed(123)
> x <- rnorm(25, mean = 1)
> x[sample(1:25, 5)] <- NA
> y <- rnorm(20, mean = -1)
> y[sample(1:20, 4)] <- NA
> pair <- c(rnorm(25, mean = 1), rnorm(20, mean = -1))
> g <- factor(c(rep("yes", 25), rep("no", 20)))
> D <- data.frame(ID = 1:45, variable = c(x, y), pair = pair, group = g)
> 
> ## Use Amelia to impute missing values
> library(Amelia)
Error in library(Amelia) : there is no package called ‘Amelia’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MKinfer.Rmd’ using rmarkdown
Quitting from lines 240-279 (MKinfer.Rmd) 
Error: processing vignette ‘MKinfer.Rmd’ failed with diagnostics:
there is no package called 'Amelia'
--- failed re-building ‘MKinfer.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'lmtest', 'saemix'

Package suggested but not available for checking: ‘benchmarkme’

See section ‘The DESCRIPTION file’ 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.
mkle: no visible global function definition for ‘sd’
mkle: no visible global function definition for ‘density’
mkle: no visible global function definition for ‘optimize’
mkle.ci: no visible global function definition for ‘sd’
mkle.ci: no visible binding for global variable ‘var’
mkle.ci: no visible global function definition for ‘quantile’
mkle.ci: no visible global function definition for ‘qnorm’
opt.bw: no visible global function definition for ‘sd’
opt.bw : mse: no visible global function definition for ‘var’
opt.bw: no visible global function definition for ‘optimize’
opt.bw: no visible global function definition for ‘var’
Undefined global functions or variables:
  density optimize qnorm quantile sd var
Consider adding
  importFrom("stats", "density", "optimize", "qnorm", "quantile", "sd",
             "var")
to your NAMESPACE file.
Packages suggested but not available for checking: 'Amelia', 'doParallel'
Package unavailable to check Rd xrefs: ‘genefilter’
Running examples in ‘MKmisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mi.t.test
> ### Title: Multiple Imputation Student's t-Test
> ### Aliases: mi.t.test mi.t.test.default
> ### Keywords: htest
> 
> ### ** Examples
> 
> ## Generate some data
> set.seed(123)
> x <- rnorm(25, mean = 1)
> x[sample(1:25, 5)] <- NA
> y <- rnorm(20, mean = -1)
> y[sample(1:20, 4)] <- NA
> pair <- c(rnorm(25, mean = 1), rnorm(20, mean = -1))
> g <- factor(c(rep("yes", 25), rep("no", 20)))
> D <- data.frame(ID = 1:45, variable = c(x, y), pair = pair, group = g)
> 
> ## Use Amelia to impute missing values
> library(Amelia)
Error in library(Amelia) : there is no package called ‘Amelia’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MKmisc.Rmd’ using rmarkdown
Quitting from lines 466-505 (MKmisc.Rmd) 
Error: processing vignette ‘MKmisc.Rmd’ failed with diagnostics:
there is no package called 'Amelia'
--- failed re-building ‘MKmisc.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'Rglpk', 'ROI.plugin.glpk'
Package required but not available: ‘ComplexHeatmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'qqplotr', 'coin'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
‘gs+qpdf’ made some significant size reductions:
     compacted ‘ml2p_vae_vignette.pdf’ from 381Kb to 130Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files
'LazyData' is specified without a 'data' directory
Package required but not available: ‘MultiLCIRT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'klaR', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'klaR', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ConfusionTableR', 'rsample', 'recipes', 'caret', 'OddsPlotty'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘snowfall’
Packages required but not available: 'ergm', 'GGally', 'sna'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fitdistrplus’
Running examples in ‘mle.tools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coxsnell.bc
> ### Title: Bias-Corrected Maximum Likelihood Estimate(s)
> ### Aliases: coxsnell.bc
> 
> ### ** Examples
> 
> {library(mle.tools); library(fitdistrplus); set.seed(1)};
Error in library(fitdistrplus) : 
  there is no package called ‘fitdistrplus’
Execution halted
Package required but not available: ‘fGarch’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘brnn’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'car', 'coxme'

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
Packages suggested but not available for checking:
  'minfi', 'GEOquery', 'IlluminaHumanMethylation450kmanifest'
Packages required but not available: 'multcomp', 'coxme', 'sommer'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘doParallel’
Packages required but not available:
  'quantspec', 'Rfast', 'TSclust', 'forecast', 'tseries', 'TSA',
  'tsfeatures', 'freqdom', 'dtw', 'complexplus', 'MTS', 'fda.usc',
  'TSdist', 'evolqg', 'DescTools', 'ClusterR', 'AID', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BMA', 'maxLik'

Package suggested but not available for checking: ‘mlogit’

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

Packages suggested but not available for checking: 'car', 'AER'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘C50’
Package required but not available: ‘caret’

Package suggested but not available for checking: ‘CORElearn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'mlr3', 'mlr3learners', 'PMCMRplus'
Package required but not available: ‘mlr3’

Package suggested but not available for checking: ‘ClusterR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mlr3’
Package required but not available: ‘mlr3’

Packages suggested but not available for checking:
  'RSQLite', 'duckdb', 'future.apply', 'future.callr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mlr3’

Packages suggested but not available for checking:
  'care', 'caret', 'mlr3learners'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mlr3', 'bbotk', 'mlr3pipelines'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mlr3tuning', 'bbotk', 'mlr3'

Packages suggested but not available for checking:
  'mlr3learners', 'mlr3pipelines'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mlr3’

Packages suggested but not available for checking: 'glmnet', 'mlr3proba'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mlr3’

Packages suggested but not available for checking: 'farff', 'mlr3proba'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mlr3’

Packages suggested but not available for checking:
  'glmnet', 'lme4', 'bbotk', 'mlr3filters', 'mlr3learners',
  'bestNormalize', 'NMF', 'vtreat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mlr3’

Packages suggested but not available for checking:
  'bujar', 'mlr3pipelines', 'survAUC'

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

Package suggested but not available for checking: ‘future.callr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mlr3', 'mlr3learners'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mlr3’

Packages suggested but not available for checking:
  'future.callr', 'mlr3learners', 'mlr3tuning', 'raster', 'rgdal',
  'stars'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mlr3’

Packages suggested but not available for checking:
  'bbotk', 'blockCV', 'caret', 'CAST', 'mlr3filters', 'mlr3pipelines',
  'mlr3tuning', 'plotly', 'raster', 'rgdal', 'sperrorest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mlr3', 'bbotk'

Package suggested but not available for checking: ‘mlr3pipelines’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mlr3tuning', 'mlr3'

Packages suggested but not available for checking: 'glmnet', 'mlr3learners'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'mlr3', 'bbotk', 'mlr3cluster', 'mlr3filters', 'mlr3fselect',
  'mlr3hyperband', 'mlr3learners', 'mlr3pipelines', 'mlr3proba',
  'mlr3tuning', 'mlr3tuningspaces', 'mlr3viz'

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

Packages suggested but not available for checking:
  'bbotk', 'factoextra', 'GGally', 'ggfortify', 'ggparty', 'glmnet',
  'mlr3', 'mlr3cluster', 'mlr3filters', 'mlr3learners', 'mlr3proba',
  'mlr3tuning', 'partykit'

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

Packages suggested but not available for checking:
  'care', 'party', 'mRMRe', 'randomForestSRC', 'Rfast', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bbotk', 'mlr3tuning'

Packages suggested but not available for checking:
  'mlr', 'cmaesr', 'smoof', 'mlr3', 'mlr3learners', 'mlr3pipelines',
  'mlrMBO'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mlr', 'smoof'

Packages suggested but not available for checking:
  'cmaesr', 'earth', 'GGally', 'party'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ada', 'adabag', 'bartMachine', 'bit64', 'brnn', 'bst', 'C50',
  'care', 'caret', 'ClusterR', 'clusterSim', 'crs', 'Cubist', 'earth',
  'elasticnet', 'evtree', 'extraTrees', 'fda.usc', 'FDboost',
  'forecast', 'fpc', 'ggpubr', 'glmnet', 'Hmisc', 'klaR', 'laGP',
  'mboost', 'mda', 'mlrMBO', 'mRMRe', 'pamr', 'party', 'pec',
  'penalized', 'PMCMRplus', 'randomForestSRC', 'refund', 'rknn',
  'rrlda', 'RSNNS', 'sda', 'smoof', 'sparseLDA', 'survAUC', 'tgp',
  'TH.data', 'tsfeatures'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mlr.Rcheck/00install.out’ for details.
Packages required but not available:
  'mlt', 'multcomp', 'flexsurv', 'truncreg', 'np'

Packages suggested but not available for checking:
  'basefun', 'TH.data', 'prodlim', 'latticeExtra', 'coxinterval',
  'bshazard', 'MIICD', 'TransModel', 'timereg', 'survivalMPL',
  'gamlss', 'ICE', 'AER', 'coin', 'tram', 'rms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'basefun', 'alabama'

Packages suggested but not available for checking: 'TH.data', 'multcomp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lme4', 'arm', 'qgraph', 'clusterGeneration', 'MplusAutomation',
  'graphicalVAR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mlxR.Rcheck/00install.out’ for details.
Package required but not available: ‘Biobase’

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

Package suggested but not available for checking: ‘MM2Sdata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'mma', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'mosaic', 'mosaicCalc'
Package required but not available: ‘rmio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xts', 'leaflet', 'plotly'

Package suggested but not available for checking: ‘devtools’

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

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

Packages suggested but not available for checking:
  'devtools', 'caret', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mmc.Rcheck/00install.out’ for details.
Package required but not available: ‘randtoolbox’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Biobase’

Package suggested but not available for checking: ‘ALL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mme.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mmm2.Rcheck/00install.out’ for details.
Packages required but not available: 'adegenet', 'pegas'

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
'LazyData' is specified without a 'data' directory
Packages required but not available: 'magic', 'emulator'

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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘sn’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘CDM’

Packages which this enhances but not available for checking:
  'aMNLFA', 'GPCMlasso', 'sirt'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ICSNP', 'ICS'

Packages suggested but not available for checking: 'Flury', 'gamlss'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘semTools’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MNP.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mnreadR.Rcheck/00install.out’ for details.
Packages required but not available: 'glmnet', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'mailR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'texmex', 'copBasic', 'ks', 'SpatialExtremes', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'EMMREML', 'doMPI', 'doRNG', 'sommer', 'vcfR', 'biomaRt',
  'doParallel', 'optiSel', 'alstructure'

Packages which this enhances but not available for checking:
  'miraculix', 'MoBPSmaps'
Package required but not available: ‘egg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MOCCA.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Modalclust.Rcheck/00install.out’ for details.
Packages required but not available:
  'dygraphs', 'highcharter', 'leaflet', 'plotly', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fBasics', 'stable'

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

Packages suggested but not available for checking:
  'TH.data', 'strucchange', 'ggbeeswarm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'brms', 'gamm4', 'gganimate', 'glmmTMB', 'lme4', 'merTools',
  'rstanarm', 'rtdists'
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RSQLite’
Error(s) in re-building vignettes:
  ...
--- re-building ‘kmeans.Rmd’ using rmarkdown
Quitting from lines 32-38 (kmeans.Rmd) 
Error: processing vignette ‘kmeans.Rmd’ failed with diagnostics:
error in evaluating the argument ‘drv’ in selecting a method for function ‘dbConnect’: there is no package called 'RSQLite'
--- failed re-building ‘kmeans.Rmd’

--- re-building ‘linear-regression.Rmd’ using rmarkdown
Quitting from lines 35-46 (linear-regression.Rmd) 
Error: processing vignette ‘linear-regression.Rmd’ failed with diagnostics:
error in evaluating the argument ‘drv’ in selecting a method for function ‘dbConnect’: there is no package called 'RSQLite'
--- failed re-building ‘linear-regression.Rmd’

SUMMARY: processing the following files failed:
  ‘kmeans.Rmd’ ‘linear-regression.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'auditor', 'archivist', 'devtools'

Package suggested but not available for checking: ‘useful’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ClassDiscovery', 'ClassComparison', 'TailRank'

Package suggested but not available for checking: ‘Biobase’

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

Package suggested but not available for checking: ‘recipes’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'rgdal', 'fields'

Packages suggested but not available for checking:
  'party', 'quantregForest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'mlr', 'caret', 'glmnet'
Running examples in ‘modelplotr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: customize_plot_text
> ### Title: Customize textual elements of the plots
> ### Aliases: customize_plot_text
> 
> ### ** Examples
> 
> # load example data (Bank clients with/without a term deposit - see ?bank_td for details)
> data("bank_td")
> 
> # prepare data for training model for binomial target has_td and train models
> train_index =  sample(seq(1, nrow(bank_td)),size = 0.5*nrow(bank_td) ,replace = FALSE)
> train = bank_td[train_index,c('has_td','duration','campaign','pdays','previous','euribor3m')]
> test = bank_td[-train_index,c('has_td','duration','campaign','pdays','previous','euribor3m')]
> 
> #train models using caret... (or use mlr or H2o or keras ... see ?prepare_scores_and_ntiles)
> # setting caret cross validation, here tuned for speed (not accuracy!)
> fitControl <- caret::trainControl(method = "cv",number = 2,classProbs=TRUE)
Error in loadNamespace(x) : there is no package called ‘caret’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘modelplotr.Rmd’ using rmarkdown
Quitting from lines 198-216 (modelplotr.Rmd) 
Error: processing vignette ‘modelplotr.Rmd’ failed with diagnostics:
there is no package called 'mlr'
--- failed re-building ‘modelplotr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'ggDCA', 'rms'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/modelROC.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'betareg', 'broom.mixed', 'gamlss', 'lfe', 'lme4', 'lmtest', 'survey'
Packages required but not available:
  'modeltime', 'modeltime.resample', 'tune', 'rsample', 'recipes',
  'timetk', 'doParallel'

Packages suggested but not available for checking:
  'dials', 'glmnet', 'earth', 'tidymodels', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'modeltime', 'timetk'

Packages suggested but not available for checking:
  'tidyverse', 'tidymodels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'modeltime', 'timetk'

Packages suggested but not available for checking:
  'tidymodels', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'timetk', 'dials', 'plotly', 'doParallel', 'forecast', 'prophet'

Packages suggested but not available for checking:
  'rstan', 'tidymodels', 'workflowsets', 'recipes', 'rsample', 'tune',
  'tidyverse', 'glmnet', 'thief', 'smooth', 'earth', 'tidyquant',
  'TSrepr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'modeltime', 'tune', 'rsample', 'recipes', 'dials', 'timetk',
  'plotly'

Packages suggested but not available for checking:
  'tidymodels', 'tidyverse', 'tidyquant', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'openintro', 'viridis', 'readr'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘markovchain’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'rgdal'

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

Package suggested but not available for checking: ‘rgdal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geojsonio', 'raster', 'xts'

Packages suggested but not available for checking:
  'httptest', 'leafem', 'leaflet', 'mapedit', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘AER’
Running examples in ‘modmarg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: marg.ivreg
> ### Title: Predicted Margins for 'ivreg' objects from the 'AER' package
> ### Aliases: marg.ivreg
> 
> ### ** Examples
> 
> # From ?AER::ivreg
> 
> # data
> data("CigarettesSW", package = "AER")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘AER’
Calls: data -> find.package
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/modMax.Rcheck/00install.out’ for details.
Packages required but not available:
  'glmnet', 'lme4', 'lmerTest', 'qgraph', 'systemfit'

Packages suggested but not available for checking: 'sn', 'arm'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'DescTools', 'C50', 'relaimpo', 'rpart.plot', 'lmtest', 'car', 'AER'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/moduleColor.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘devtools’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘smoof’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘Basic_Usage.Rmd’ using rmarkdown
Quitting from lines 106-114 (Basic_Usage.Rmd) 
Error: processing vignette ‘Basic_Usage.Rmd’ failed with diagnostics:
there is no package called 'smoof'
--- failed re-building ‘Basic_Usage.Rmd’

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

--- re-building ‘Modification_Usage.Rmd’ using rmarkdown
Quitting from lines 70-94 (Modification_Usage.Rmd) 
Error: processing vignette ‘Modification_Usage.Rmd’ failed with diagnostics:
there is no package called 'smoof'
--- failed re-building ‘Modification_Usage.Rmd’

--- re-building ‘problem-definition.Rmd’ using rmarkdown
--- finished re-building ‘problem-definition.Rmd’

--- re-building ‘writing-functions-for-moeadr.Rmd’ using rmarkdown
--- finished re-building ‘writing-functions-for-moeadr.Rmd’

SUMMARY: processing the following files failed:
  ‘Basic_Usage.Rmd’ ‘Modification_Usage.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘vcd’

Packages suggested but not available for checking: 'clustMD', 'geometry'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘poLCA’

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

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

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

Package suggested but not available for checking: ‘DSMolgenisArmadillo’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'WGCNA', 'Rfast', 'readr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lmtest’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/momentfit.Rcheck/00install.out’ for details.
agostino.test: no visible global function definition for
  ‘complete.cases’
agostino.test: no visible global function definition for ‘pnorm’
anscombe.test: no visible global function definition for
  ‘complete.cases’
anscombe.test: no visible global function definition for ‘pnorm’
bonett.test: no visible global function definition for ‘complete.cases’
bonett.test: no visible global function definition for ‘pnorm’
jarque.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  complete.cases pchisq pnorm
Consider adding
  importFrom("stats", "complete.cases", "pchisq", "pnorm")
to your NAMESPACE file.
Packages required but not available:
  'doParallel', 'CircStats', 'crawl', 'doRNG'

Packages suggested but not available for checking:
  'R.rsp', 'raster', 'conicfit', 'ggmap', 'expm', 'moveHMM',
  'doFuture', 'car', 'prodlim'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dendextend', 'geometry', 'geomorph', 'rgeos', 'vegan'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'topicmodels', 'tm', 'doParallel'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'TTmoment', 'tmvtnorm'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/monitoR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/monmlp.Rcheck/00install.out’ for details.
Package required but not available: ‘Hmisc’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'maptools', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'sitar'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/monomvn.Rcheck/00install.out’ for details.
Packages required but not available: 'phytools', 'phangorn', 'taxize'

Package suggested but not available for checking: ‘paleotree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MonoPoly.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘lmtest’

Package suggested but not available for checking: ‘xts’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ggwordcloud', 'RMariaDB', 'RSQLite', 'RPostgres'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘readr’
mopsocd : initialize_pop: no visible global function definition for
  ‘runif’
mopsocd : compute_velocity: no visible global function definition for
  ‘runif’
mopsocd : mutate: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyverse’
Error(s) in re-building vignettes:
  ...
--- re-building ‘moranajp.Rmd’ using rmarkdown
Quitting from lines 19-21 (moranajp.Rmd) 
Error: processing vignette ‘moranajp.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘moranajp.Rmd’

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

Error: Vignette re-building failed.
Execution halted
checkTH: no visible global function definition for ‘pchisq’
getOrderPval: 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
Packages required but not available:
  'party', 'partykit', 'varImp', 'iml', 'pdp'

Packages suggested but not available for checking:
  'doParallel', 'GDAtools', 'caret', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
ametrine : <anonymous>: no visible global function definition for
  ‘approx’
ametrine: no visible global function definition for ‘rgb’
isolum : <anonymous>: no visible global function definition for
  ‘approx’
isolum: no visible global function definition for ‘rgb’
morgenstemning : <anonymous>: no visible global function definition for
  ‘approx’
morgenstemning: 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
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'flexmix'
Packages required but not available:
  'Arothron', 'Morpho', 'oce', 'rgdal', 'raster', 'geometry',
  'DescTools'

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

Package suggested but not available for checking: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'candisc', 'car', 'heplots', 'StatMatch', 'vegan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/morph.Rcheck/00install.out’ for details.
Package required but not available: ‘rjags’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyverse’

Package which this enhances but not available for checking: ‘lifecontingencies’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MortalityTables.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MortCast.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'mosaic', 'ggformula'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'mosaic', 'ggformula'
'LazyData' is specified without a 'data' directory
Running examples in ‘mosaicCore-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: inspect
> ### Title: Inspect objects
> ### Aliases: inspect inspect.list inspect.character inspect.logical
> ###   inspect.numeric inspect.factor inspect.Date inspect.POSIXt
> ###   inspect.data.frame print.inspected_data_frame
> 
> ### ** Examples
> 
> if (require(mosaicData)) {
+   inspect(Births78)
+   inspect(Births78, is.numeric)
+ }
Loading required package: mosaicData
Error in loadNamespace(x) : there is no package called ‘mosaic’
Calls: inspect ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mosaicCore)
  
  Attaching package: 'mosaicCore'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  > 
  > test_check("mosaicCore")
  Failed with error:  'there is no package called 'mosaic''
  Failed with error:  'there is no package called 'mosaic''
  [ FAIL 2 | WARN 1 | SKIP 1 | PASS 78 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • empty test (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-interval-calculations.R:26:3): CI for sample proportions work. ──
  t2[c("six_lower", "six_upper")] not equivalent to as.numeric(ref$conf.int).
  Component 1: Mean relative difference: 0.01043699
  Component 2: Mean relative difference: 0.06594204
  ── Failure (test-interval-calculations.R:34:3): CI for sample proportions work with long_names. ──
  t2[c("six_lower", "six_upper")] not equivalent to as.numeric(ref$conf.int).
  Component 1: Mean relative difference: 0.01043699
  Component 2: Mean relative difference: 0.06594204
  
  [ FAIL 2 | WARN 1 | SKIP 1 | PASS 78 ]
  Error: Test failures
  Execution halted
Packages suggested but not available for checking: 'mosaic', 'ggformula'
Packages required but not available: 'caret', 'ggformula', 'tidyverse'

Package suggested but not available for checking: ‘mosaic’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggformula', 'ggrepel', 'readr', 'latticeExtra', 'leaflet'

Packages suggested but not available for checking:
  'maptools', 'vcd', 'mapproj'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ecr', 'smoof', 'mlrCPO', 'mlr'

Package suggested but not available for checking: ‘mlrMBO’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'annotate', 'bigparallelr', 'bigstatsr', 'future.apply',
  'scatterpie', 'clValid', 'ComplexHeatmap', 'fpc', 'ggpmisc', 'irlba',
  'viridis', 'VennDiagram'
Error(s) in re-building vignettes:
  ...
--- re-building ‘MOSS_working_example.Rmd’ using rmarkdown
Quitting from lines 134-144 (MOSS_working_example.Rmd) 
Error: processing vignette ‘MOSS_working_example.Rmd’ failed with diagnostics:
there is no package called 'viridis'
--- failed re-building ‘MOSS_working_example.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'MBESS', 'ez'

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

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

Package suggested but not available for checking: ‘spdep’

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

Package suggested but not available for checking: ‘ergm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ks', 'caper'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (7) predict.moult.Rd:51: \item in \value must have non-empty label
checkRd: (7) predict.moult.Rd:53: \item in \value must have non-empty label
Package suggested but not available for checking: ‘latticeExtra’
Error(s) in re-building vignettes:
  ...
--- re-building ‘mountainplot_examples.Rmd’ using rmarkdown
Quitting from lines 49-54 (mountainplot_examples.Rmd) 
Error: processing vignette ‘mountainplot_examples.Rmd’ failed with diagnostics:
could not find function "ecdfplot"
--- failed re-building ‘mountainplot_examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mousetrack.Rcheck/00install.out’ for details.
Packages required but not available: 'cstab', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'gdistance', 'elevatr', 'maptools', 'raster', 'rgdal', 'rgeos',
  'spatstat.geom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'CircStats', 'ggmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'rgdal'

Packages suggested but not available for checking:
  'adehabitatHR', 'adehabitatLT', 'ggmap', 'mapproj', 'maptools',
  'leaflet', 'ctmm', 'amt', 'bcpa', 'EMbC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'move', 'raster', 'slippymath'

Packages suggested but not available for checking: 'mapview', 'leaflet'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'tm', 'vcd', 'corpus.useR.2008.abstracts', 'flexmix'
Error(s) in re-building vignettes:
  ...
--- re-building ‘movMF.Rnw’ using Sweave
trying URL ‘https://datacube.wu.ac.at/src/contrib/corpus.useR.2008.abstracts_2009.08.10.tar.gz’
Content type 'application/x-gzip' length 98736 bytes (96 KB)
==================================================
downloaded 96 KB

* installing *source* package ‘corpus.useR.2008.abstracts’ ...
** using staged installation
** data
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (corpus.useR.2008.abstracts)

The downloaded source packages are in
	'/home/hornik/tmp/scratch/RtmpitYeSF/downloaded_packages'

Error: processing vignette ‘movMF.Rnw’ failed with diagnostics:
 chunk 12 
Error in library("tm") : there is no package called 'tm'

--- failed re-building 'movMF.Rnw'

SUMMARY: processing the following file failed:
  'movMF.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'R.utils', 'changepoint', 'glmnet', 'HDPenReg'

Packages suggested but not available for checking:
  'CGHcall', 'aroma.affymetrix', 'aroma.cn', 'aroma.core',
  'aroma.light', 'snowfall', 'R.devices', 'R.filesets', 'R.oo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'pamr', 'doParallel', 'bst'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cvTools', 'mlogit'

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

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mpcv.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mpe.Rcheck/00install.out’ for details.
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MPINet.Rcheck/00install.out’ for details.
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'markovchain', 'matlib'
'LazyData' is specified without a 'data' directory
Running examples in ‘MPkn-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MPkn-package
> ### Title: Calculations of One Discrete Model in Several Time Steps
> ### Aliases: MPkn-package
> 
> ### ** Examples
> 
> require(MPkn)
> require(markovchain)
Loading required package: markovchain
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘markovchain’
> options(digits = 14)
> n = 12
> k = 2
> rz = 11
> P = array(0, c(rz, rz))
> for (i in 1:rz){
+   po = runif(rz)
+   P[i, ] = po/sum(po)
+ }
> I = diag(1, rz, rz)
> Myy = MUPkL(P, P, I, n, k, c(1:rz))
> StSy = NULL
> for (i in 1:rz) StSy = c(StSy, Myy$Navg[,,i][n])
> mrkv = new("markovchain", transitionMatrix = P)
Error in getClass(Class, where = topenv(parent.frame())) : 
  “markovchain” is not a defined class
Calls: new -> getClass
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MPLikelihoodWB.Rcheck/00install.out’ for details.
Packages required but not available:
  'bestglm', 'doParallel', 'doRNG', 'glmnet'

Packages suggested but not available for checking: 'mvoutlier', 'glmulti'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'MplusAutomation', 'rpart.plot'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mpmi.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘orthopolynom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
place: no visible global function definition for ‘points’
plot,mproc: no visible binding for global variable ‘rainbow’
plot,mproc: no visible global function definition for ‘plot.default’
plot,mproc: no visible global function definition for ‘axis’
plot,mproc: no visible global function definition for ‘points’
Undefined global functions or variables:
  axis plot.default points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "plot.default", "points")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MPR.genotyping.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘caper’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MPSEM.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘snowfall’
Packages required but not available: 'TreeBUGS', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'raster', 'rasterVis', 'latticeExtra', 'viridis'

Packages suggested but not available for checking: 'rgdal', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MPV.Rcheck/00install.out’ for details.
Packages required but not available: 'pch', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mQTL.Rcheck/00install.out’ for details.
Package required but not available: ‘multcomp’

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

Packages suggested but not available for checking:
  'rjags', 'tidyverse', 'ggmcmc', 'DescTools', 'bayesmeta',
  'MendelianRandomization'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MRCE.Rcheck/00install.out’ for details.
Package required but not available: ‘geojsonio’

Packages suggested but not available for checking:
  'rgdal', 'rgeos', 'rmapshaper'

Package which this enhances but not available for checking: ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fields', 'glmnet', 'randtoolbox'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'caret'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'monmlp', 'nnfor'

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

Package suggested but not available for checking: ‘arrow’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mrgsim.sa.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘pmxTools’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MRHawkes.Rcheck/00install.out’ for details.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MRH.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mritc.Rcheck/00install.out’ for details.
Package required but not available: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'coin', 'doParallel', 'mrMLM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'coin', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mRMRe.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mro.Rcheck/00install.out’ for details.
Packages required but not available:
  'GGally', 'graph', 'Hmisc', 'pcalg', 'Rgraphviz', 'sna', 'WGCNA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘rstan’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mrregression.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MRsurv.Rcheck/00install.out’ for details.
Package required but not available: ‘magic’

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

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

Package suggested but not available for checking: ‘doParallel’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
msap: no visible global function definition for ‘packageVersion’
msap: no visible global function definition for ‘read.csv’
msap: no visible global function definition for ‘write.csv’
msap: no visible global function definition for ‘sd’
msap: no visible global function definition for ‘wilcox.test’
msap: no visible global function definition for ‘dist’
msap: no visible global function definition for ‘rainbow’
msap: no visible global function definition for ‘png’
msap: no visible global function definition for ‘legend’
msap: no visible global function definition for ‘dev.off’
pcoa: no visible global function definition for ‘cmdscale’
pcoa: no visible global function definition for ‘png’
pcoa: no visible global function definition for ‘par’
pcoa: no visible global function definition for ‘rainbow’
pcoa: no visible global function definition for ‘points’
pcoa: no visible global function definition for ‘dev.off’
pcoa: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  cmdscale dev.off dist legend packageVersion par png points rainbow
  read.csv sd wilcox.test write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png", "rainbow")
  importFrom("graphics", "legend", "par", "points")
  importFrom("stats", "cmdscale", "dist", "sd", "wilcox.test")
  importFrom("utils", "packageVersion", "read.csv", "write.csv")
to your NAMESPACE file.
Package suggested but not available for checking: ‘Biostrings’
Package unavailable to check Rd xrefs: ‘Biostrings’
Packages required but not available: 'ggfortify', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Packages required but not available:
  'MALDIrppa', 'MALDIquantForeign', 'mixOmics', 'caret', 'VSURF',
  'metap', 'glmnet'

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

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

Packages suggested but not available for checking:
  'GA', 'Rmalschains', 'hydroPSO'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MScombine.Rcheck/00install.out’ for details.
Packages required but not available: 'phangorn', 'doParallel'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/msda.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘snowfall’

Packages suggested but not available for checking:
  'devtools', 'ggrepel', 'rfishbase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'nnfor', 'MSGARCH', 'forecast'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘test.txt’
Package suggested but not available for checking: ‘sna’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggbeeswarm’

Package suggested but not available for checking: ‘caret’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'changepoint', 'forecast', 'Rssa', 'tseries'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/msme.Rcheck/00install.out’ for details.
Package required but not available: ‘expm’

Packages suggested but not available for checking:
  'mstate', 'doParallel', 'flexsurv'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/msos.Rcheck/00install.out’ for details.
Packages required but not available: 'ggpubr', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘MSQC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: covariance
> ### Title: Sample covariance
> ### Aliases: covariance
> 
> ### ** Examples
> 
> # individual case 
> data(bimetal1)
> covariance(bimetal1, method = "sw")
Error in class(x) == "matrix" || class(x) == "data.frame" : 
  'length = 2' in coercion to 'logical(1)'
Calls: covariance
Execution halted
Package suggested but not available for checking: ‘tidyverse’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Ecdat’
Package suggested but not available for checking: ‘haven’
Running examples in ‘msSPChelpR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calc_futime
> ### Title: Calculate follow-up time per case until end of follow-up
> ###   depending on pat_status - tidyverse version
> ### Aliases: calc_futime
> 
> ### ** Examples
> 
> #load sample data
> data("us_second_cancer")
> 
> #prep step - make wide data as this is the required format
> usdata_wide <- us_second_cancer %>%
+                     msSPChelpR::reshape_wide_tidyr(case_id_var = "fake_id", 
+                     time_id_var = "SEQ_NUM", timevar_max = 10)
>                     
> #prep step - calculate p_spc variable
> usdata_wide <- usdata_wide %>%
+                  dplyr::mutate(p_spc = dplyr::case_when(is.na(t_site_icd.2)   ~ "No SPC",
+                                                        !is.na(t_site_icd.2)   ~ "SPC developed",
+                                                        TRUE ~ NA_character_)) %>%
+                  dplyr::mutate(count_spc = dplyr::case_when(is.na(t_site_icd.2)   ~ 1,
+                                                               TRUE ~ 0))
>                                                               
> #prep step - create patient status variable
> usdata_wide <- usdata_wide %>%
+                   msSPChelpR::pat_status(., fu_end = "2017-12-31", dattype = "seer",
+                                          status_var = "p_status", life_var = "p_alive.1",
+                                          birthdat_var = "datebirth.1", lifedat_var = "datedeath.1")
Error in set_labels_helper(x = x[[vars[i]]], labels = labels[[i]], force.labels = force.labels,  : 
  Package 'haven' required for this function. Please install it.
Calls: %>% ... <Anonymous> -> %>% -> <Anonymous> -> set_labels_helper
Execution halted
Running ‘testthat.R’ [5s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(msSPChelpR)
  > 
  > test_check("msSPChelpR")
  Long dataset had too many cases per patient. Wide dataset is limited to  2  cases per id as defined in timevar_max option.
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 3 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-pat_status.R:5:3): custom variable name for status_var works ────
  Error in `set_labels_helper(x = x[[vars[i]]], labels = labels[[i]], force.labels = force.labels, 
      force.values = force.values, drop.na = drop.na, var.name = vars[i])`: Package 'haven' required for this function. Please install it.
  Backtrace:
      ▆
   1. ├─... %>% ... at test-pat_status.R:5:2
   2. ├─msSPChelpR::pat_status(...)
   3. │ └─... %>% ...
   4. └─sjlabelled::val_labels(...)
   5.   └─sjlabelled:::set_labels_helper(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 3 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 177-205 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
Package 'haven' required for this function. Please install it.
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘graph’

Package suggested but not available for checking: ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'cmprsk', 'relsurv'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mstate.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'expm', 'mirt', 'scDIFtest'

Package suggested but not available for checking: ‘strucchange’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'nls2'

Package suggested but not available for checking: ‘RSQLite’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘httptest’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mapsf’
Running examples in ‘MTA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gdev
> ### Title: General Deviation
> ### Aliases: gdev
> 
> ### ** Examples
> 
> # Load data
> library(mapsf)
Error in library(mapsf) : there is no package called ‘mapsf’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MTA.Rmd’ using rmarkdown
--- finished re-building ‘MTA.Rmd’

--- re-building ‘MTA_Scenario.Rmd’ using rmarkdown
Quitting from lines 54-65 (MTA_Scenario.Rmd) 
Error: processing vignette ‘MTA_Scenario.Rmd’ failed with diagnostics:
there is no package called 'mapsf'
--- failed re-building ‘MTA_Scenario.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘dtw’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'quantreg', 'glmnet', 'rqPen'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mthapower
> ### Title: Power calculations - mtDNA haplogroups
> ### Aliases: mthapower
> 
> ### ** Examples
> 
> # Example 1:
> pow <- mthapower(n.cases=203, p0=0.443, Nh=13, OR.cas.ctrl=2.33, sig.level=0.05)
> 
> # Example 2:
> # Create data frames
> pow.H150 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=1.5, sig.level=0.05)
> pow.H175 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=1.75, sig.level=0.05)
> pow.H200 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=2, sig.level=0.05)
> pow.H250 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=2.5, sig.level=0.05)
> 
> # Bind the three data frames:
> bindata <- rbind(pow.H150,pow.H175,pow.H200,pow.H250)
> # Adds column OR to binded data frame:
> bindata$OR <- rep(factor(c(1.50,1.75,2,2.5)),
+               times = c(nrow(pow.H150),
+                         nrow(pow.H175),
+                         nrow(pow.H200),
+                         nrow(pow.H250)))
> # Create plot:
> # install.packages("car")
> library(car)
Error in library(car) : there is no package called ‘car’
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mtk.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘glmnet’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'imager', 'dplR', 'spatstat.geom', 'measuRing'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fGarch', 'fBasics'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘epiDisplay’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MuFiCokriging.Rcheck/00install.out’ for details.
Packages required but not available:
  'splancs', 'Hmisc', 'rgeos', 'tidyverse'

Package suggested but not available for checking: ‘plotly’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'geometry', 'mirt', 'Hmisc', 'car', 'dae'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/multbxxc.Rcheck/00install.out’ for details.
Package required but not available: ‘TH.data’

Packages suggested but not available for checking:
  'lme4', 'coin', 'lmtest', 'coxme', 'SimComp', 'tram'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'multcomp', 'pgirmess'
Running examples in ‘multcompView-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: multcompBoxplot
> ### Title: boxplot with multcomp graphics
> ### Aliases: multcompBoxplot
> ### Keywords: aplot
> 
> ### ** Examples
> 
> 
> # Example from help("TukeyHSD")
> multcompBoxplot(breaks~tension, data=warpbreaks)
> # 'sortFn' can be either a function or a function name
> # default order is 'decreasing=TRUE'
> multcompBoxplot(breaks~tension, data=warpbreaks,
+        sortFn=median, decreasing=FALSE)
> 
> ##################
> library(multcomp)
Error in library(multcomp) : there is no package called ‘multcomp’
Execution halted
Package suggested but not available for checking: ‘SimComp’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/multgee.Rcheck/00install.out’ for details.
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'readr', 'magic', 'powerplus', 'neldermead'
Running examples in ‘MultiATSM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GVAR
> ### Title: Estimate a GVAR(1) and a VARX(1,1,1)
> ### Aliases: GVAR
> 
> ### ** Examples
> 
> data(CM_Factors_GVAR)
> 
> N <- 3
> 
> GVARinputs <- list()
> GVARinputs$Economies <- c("China", "Brazil", "Mexico", "Uruguay")
> GVARinputs$GVARFactors <- FactorsGVAR
> GVARinputs$VARXtype <- "unconstrained"
> GVARinputs$Wgvar <- matrix( c(0, 0.83, 0.86, 0.38,
+                               0.65, 0, 0.13, 0.55,
+                               0.32, 0.12, 0, 0.07,
+                               0.03, 0.05, 0.01, 0), nrow = 4, ncol = 4)
> 
> GVAR(GVARinputs, N)
Error in loadNamespace(x) : there is no package called ‘magic’
Calls: GVAR ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Quitting from lines 347-358 (my-vignette.Rmd) 
Error: processing vignette ‘my-vignette.Rmd’ failed with diagnostics:
there is no package called 'magic'
--- failed re-building ‘my-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
synthetic_multiband: no visible global function definition for ‘runif’
synthetic_multiband: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: ‘MCMCpack’
Packages required but not available:
  'car', 'FactoMineR', 'lme4', 'mixlm', 'plsVarSel', 'SSBtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Package required but not available: ‘multcomp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plotly’

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

Packages suggested but not available for checking:
  'Biobase', 'switchBox', 'leukemiasEset'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
calculate_direction: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/multicon.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/multicool.Rcheck/00install.out’ for details.
Packages required but not available: 'nbpMatching', 'crossmatch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'pcaMethods'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘vroom’
Error(s) in re-building vignettes:
  ...
--- re-building ‘multidplyr.Rmd’ using rmarkdown
Quitting from lines 63-69 (multidplyr.Rmd) 
Error: processing vignette ‘multidplyr.Rmd’ failed with diagnostics:
there is no package called 'vroom'
--- failed re-building ‘multidplyr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'glmnet', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'funData', 'MFPCA', 'sparseFLMM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ez', 'BayesFactor', 'forestplot'

Package suggested but not available for checking: ‘ggraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘qgraph’
Error(s) in re-building vignettes:
  ...
--- re-building ‘MultiFIT.Rmd’ using rmarkdown
Quitting from lines 103-107 (MultiFIT.Rmd) 
Error: processing vignette ‘MultiFIT.Rmd’ failed with diagnostics:
there is no package called 'qgraph'
--- failed re-building ‘MultiFIT.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/multigraph.Rcheck/00install.out’ for details.
Packages required but not available:
  'expm', 'plsgenomics', 'ggrepel', 'qgraph', 'mgm'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MultiLCIRT.Rcheck/00install.out’ for details.
Package required but not available: ‘lme4’

Packages suggested but not available for checking: 'contrast', 'tidymodels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'PSAgraphics', 'party'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/multilevel.Rcheck/00install.out’ for details.
Packages required but not available: 'lme4', 'lmerTest', 'JWileymisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'RMark', 'prodlim', 'raster'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyverse', 'devtools', 'sqldf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/multinet.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'sand', 'statnet'
Packages required but not available:
  'rstan', 'randtoolbox', 'ggraph', 'truncdist'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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

Package suggested but not available for checking: ‘rPorta’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MultiOrd.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'ComplexHeatmap', 'VennDiagram'
Package unavailable to check Rd xrefs: ‘ComplexHeatmap’
Packages required but not available: 'meta', 'HardyWeinberg'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/multipleNCC.Rcheck/00install.out’ for details.
Package required but not available: ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'multigraph', 'Rgraphviz'
Error(s) in re-building vignettes:
  ...
--- re-building ‘TwoModeNetworks.Rnw’ using knitr
Quitting from lines 128-132 (TwoModeNetworks.Rnw) 
Error: processing vignette ‘TwoModeNetworks.Rnw’ failed with diagnostics:
there is no package called 'Rgraphviz'
--- failed re-building ‘TwoModeNetworks.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MultiplierDEA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/multipol.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'risksetROC', 'snowfall'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘quantreg’
Running examples in ‘MultiRobust-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MR.quantile
> ### Title: Multiply Robust Estimation of the Marginal Quantile
> ### Aliases: MR.quantile
> 
> ### ** Examples
> 
> # Simulated data set
> set.seed(123)
> n <- 400
> gamma0 <- c(1, 2, 3)
> alpha0 <- c(-0.8, -0.5, 0.3)
> X <- runif(n, min = -2.5, max = 2.5)
> p.mis <- 1 / (1 + exp(alpha0[1] + alpha0[2] * X + alpha0[3] * X ^ 2))
> R <- rbinom(n, size = 1, prob = 1 - p.mis)
> a.x <- gamma0[1] + gamma0[2] * X + gamma0[3] * exp(X)
> Y <- rnorm(n, a.x, sd = sqrt(4 * X ^ 2 + 2))
> dat <- data.frame(X, Y)
> dat[R == 0, 2] <- NA
> 
> # Define the outcome regression models and missingness probability models
> imp1 <- glm.work(formula = Y ~ X + exp(X), family = gaussian)
> imp2 <- glm.work(formula = Y ~ X + I(X ^ 2), family = gaussian)
> mis1 <- glm.work(formula = R ~ X + I(X ^ 2), family = binomial(link = logit))
> mis2 <- glm.work(formula = R ~ X + exp(X), family = binomial(link = cloglog))
> MR.quantile(response = Y, tau = 0.25, imp.model = list(imp1, imp2),
+             mis.model = list(mis1, mis2), L = 10, data = dat)
Error in MR.quantile(response = Y, tau = 0.25, imp.model = list(imp1,  : 
  need CRAN package 'quantreg' for quantile estimation
Execution halted
Package required but not available: ‘lme4’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'AROC', 'coxme', 'lme4', 'lmerTest', 'metafor'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MultiSkew.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/multisom.Rcheck/00install.out’ for details.
CCM_boot : <anonymous>: no visible global function definition for ‘sd’
SSR_check_signal: no visible global function definition for ‘cor’
SSR_check_signal: no visible global function definition for ‘cor.test’
SSR_check_signal: no visible global function definition for ‘lm’
SSR_pred_boot: no visible global function definition for ‘cor’
make_ccm_data: no visible global function definition for ‘rnorm’
make_ccm_data: no visible global function definition for ‘runif’
make_ccm_data: no visible global function definition for ‘rlnorm’
Undefined global functions or variables:
  cor cor.test lm rlnorm rnorm runif sd
Consider adding
  importFrom("stats", "cor", "cor.test", "lm", "rlnorm", "rnorm",
             "runif", "sd")
to your NAMESPACE file.
Packages required but not available: 'clValid', 'clv', 'ltm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
PrbMlt.default: no visible binding for global variable ‘na.omit’
PrbMlt.default: no visible global function definition for ‘anova’
Undefined global functions or variables:
  anova na.omit
Consider adding
  importFrom("stats", "anova", "na.omit")
to your NAMESPACE file.
Package suggested but not available for checking: ‘astrochron’
Package suggested but not available for checking: ‘CCA’
Packages required but not available: 'candisc', 'biotools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'BinOrdNonNor', 'CorrToolBox', 'PoisNonNor'

Package suggested but not available for checking: ‘PoisBinOrdNonNor’

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

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

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'gganimate', 'styler'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/multiverse.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘CMLS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lmtest’
Running examples in ‘multiwayvcov-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cluster.vcov
> ### Title: Multi-way standard error clustering
> ### Aliases: cluster.vcov
> ### Keywords: clustering errors multi-way robust standard
> 
> ### ** Examples
> 
> library(lmtest)
Error in library(lmtest) : there is no package called ‘lmtest’
Execution halted
Package required but not available: ‘ICSNP’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/multxpert.Rcheck/00install.out’ for details.
Packages required but not available: 'car', 'rrcov'

Depends: includes the non-default packages:
  'car', 'pdist', 'pls', 'gplots', 'mvtnorm', 'robustbase', 'gtools',
  'bitops', 'caTools', 'pcaPP', 'rrcov'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'lme4', 'gamm4'

Packages which this enhances but not available for checking:
  'aods3', 'betareg', 'caper', 'coxme', 'cplm', 'MCMCglmm', 'spdep',
  'spatialreg', 'splm', 'unmarked', 'geeM', 'gamlss'
Package required but not available: ‘lme4’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/muRL.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘qmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plsgenomics’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/musicNMR.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘DescTools’
prentice.test: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages required but not available: 'mutoss', 'multcomp', 'JGR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'multtest', 'multcomp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Familias', 'paramlink', 'expm', 'IBDsim'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'flexclust', 'RLRsim', 'multcomp', 'sem'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MVA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MVB.Rcheck/00install.out’ for details.
Package required but not available: ‘rattle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'MNM', 'quantreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mvglmmRank.Rcheck/00install.out’ for details.
Packages required but not available: 'geometry', 'CBPS'

Package suggested but not available for checking: ‘ggdag’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'heplots'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Packages required but not available: 'fields', 'wavethresh', 'xts'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'metafor', 'meta'
Package required but not available: ‘lme4’

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

Package suggested but not available for checking: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rfast’
Running examples in ‘MVNBayesian-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MVNBayesian-package
> ### Title: Bayesian Analysis Framework for MVN (Mixture) Distribution
> ### Aliases: MVNBayesian-package MVNBayesian
> ### Keywords: package Bayesian posteriori MVN distribution MVN mixture
> ###   distribution Gibbs sampling MCMC
> 
> ### ** Examples
> 
> library(Rfast)
Error in library(Rfast) : there is no package called ‘Rfast’
Execution halted
Package required but not available: ‘car’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mvnTest.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mvord.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mvoutlier.Rcheck/00install.out’ for details.
Packages required but not available: 'mpoly', 'magic', 'disordR'

Package suggested but not available for checking: ‘spray’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
mvorpb: no visible global function definition for ‘pnorm’
mvorpb: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm pnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MVR.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'furrr', 'textmineR'
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting_started_with_mvrsquared.Rmd’ using rmarkdown
Quitting from lines 150-183 (getting_started_with_mvrsquared.Rmd) 
Error: processing vignette ‘getting_started_with_mvrsquared.Rmd’ failed with diagnostics:
there is no package called 'textmineR'
--- failed re-building ‘getting_started_with_mvrsquared.Rmd’

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

Error: Vignette re-building failed.
Execution halted
rtn: no visible global function definition for ‘runif’
rtn: no visible global function definition for ‘qnorm’
rtn: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm runif
Consider adding
  importFrom("stats", "pnorm", "qnorm", "runif")
to your NAMESPACE file.
Packages required but not available: 'PCMBase', 'TreeSim'

Packages suggested but not available for checking:
  'PCMBaseCpp', 'geiger', 'mvMORPH'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mvtsplot.Rcheck/00install.out’ for details.
Package required but not available: ‘cem’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'BioNet', 'DLBCL'
Package suggested but not available for checking: ‘penalized’
Running examples in ‘MWLasso-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MWLasso
> ### Title: Penalized Moving-Window Lasso Method for Genome-Wide Association
> ###   Studies
> ### Aliases: MWLasso MW_parameters
> ### Keywords: model fitting
> 
> ### ** Examples
> 
> # In example 1, feature matrix X and response variable Y are randomly generated.
> # Example 1:
> n = 100
> p = 200
> X = matrix(rnorm(n*p, mean = 0, sd = 1), nrow = n, ncol = p)
> X[2,1] = NA; X[80:90,1]= NA; 
> Y =  rnorm(n, mean = 0, sd = 1)
> 
> number = 20
> gamma2 = 0.1
> d = 4
> params = MW_parameters(X, Y, d, number, gamma2, method="linear")
Tuning parameters are: lambda = 0.1413146, eta = 1.271831.> lambda = params[1]
> eta = params[2]
> beta.hat = MWLasso(X, Y, lambda, eta, d, method="linear")
> 
> # In example 2, the nki70 dataset is from the "penalized" package
> # (https://cran.r-project.org/web/packages/penalized/penalized.pdf).
> # The response variable Y is "event", the disease indicator.
> # The feature matrix X is "TSPYL5...C20orf46", the gene expression
> # measurements of 70 prognostic genes.
> # Example 2:
> require("penalized")
Loading required package: penalized
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘penalized’
> data(nki70)
Warning in data(nki70) : data set ‘nki70’ not found
> data = nki70
Error: object 'nki70' not found
Execution halted
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mwshiny.Rcheck/00install.out’ for details.
Packages required but not available: 'nnTensor', 'ccTensor'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyverse’
Error(s) in re-building vignettes:
  ...
--- re-building ‘mmod_tutorial.Rmd’ using rmarkdown
Quitting from lines 42-45 (mmod_tutorial.Rmd) 
Error: processing vignette ‘mmod_tutorial.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘mmod_tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'quantreg', 'lme4', 'doParallel', 'Rfast', 'coxme', 'Rfast2', 'Hmisc'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fda', 'caret', 'uwot', 'lme4', 'kSamples', 'fossil'

See section ‘The DESCRIPTION file’ 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.
abcpred_nmer: no visible global function definition for ‘write.table’
algpred: no visible global function definition for ‘read.table’
algpred: no visible global function definition for ‘write.table’
allermatch: no visible global function definition for ‘read.table’
allermatch: no visible global function definition for ‘write.table’
bcepred_nmer: no visible global function definition for ‘write.table’
bimas_nmer: no visible global function definition for ‘write.table’
filter.firstlayer: no visible global function definition for
  ‘read.table’
filter.firstlayer: no visible global function definition for
  ‘write.table’
iedb_arb_mhci_nmer: no visible global function definition for
  ‘write.table’
iedb_arb_mhcii_nmer: no visible global function definition for
  ‘write.table’
iedb_consensus_mhci_nmer: no visible global function definition for
  ‘write.table’
iedb_consensus_mhcii_nmer: no visible global function definition for
  ‘write.table’
netmhcNN_nmer: no visible global function definition for ‘write.table’
netmhcWT_nmer: no visible global function definition for ‘write.table’
propred_nmer: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
update_episode: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
Rd file 'myepisodes_feed_url.Rd':
  \examples lines wider than 100 characters:
     ## Not run: myepisodes_feed_url("foouser", "321654321654321", feed = "mylist", onlyunacquired = TRUE, showignored = FALSE)

Rd file 'shows_from_myepisodes.Rd':
  \examples lines wider than 100 characters:
     ## Not run: shows_from_myepisodes("foouser", "321654321654321", feed = "mylist", onlyunacquired = TRUE, showignored = FALSE)

These lines will be truncated in the PDF manual.
Packages required but not available: 'car', 'lmtest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fitdistrplus', 'doParallel', 'taxize', 'readr', 'edgeR'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rms', 'mclogit'

Package suggested but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘httptest’
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(N2H4)
  > 
  > test_check("N2H4")
  Error in library(httptest) : there is no package called 'httptest'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/N2R.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'ggbeeswarm', 'ggforce', 'ggrepel'

Packages suggested but not available for checking: 'Biobase', 'GEOquery'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fitdistrplus', 'multcomp', 'NADA', 'survminer', 'cenGAM', 'vegan',
  'coin'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/NADA.Rcheck/00install.out’ for details.
Packages required but not available:
  'mlr3', 'mlr3pipelines', 'mlr3learners', 'missForest', 'missMDA',
  'doParallel', 'Amelia', 'VIM', 'softImpute', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages which this enhances but not available for checking:
  'MCMCglmm', 'asreml'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nadiv.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'mapdata', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gmm', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘re2r’
Packages required but not available: 'qrcode', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Biostrings’
Package unavailable to check Rd xrefs: ‘Biostrings’
Malformed Description field: should contain one or more complete sentences.
Packages required but not available:
  'autothresholdr', 'detrendr', 'filesstrings', 'ijtiff', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'visdat', 'viridis'

Packages suggested but not available for checking:
  'rpart.plot', 'imputeTS', 'Hmisc'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ccaPP', 'epiR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bit64’

Package suggested but not available for checking: ‘xts’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'strucchange', 'tseries', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spatialClust’
Package required but not available: ‘nat’

Package suggested but not available for checking: ‘ff’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'alphashape3d', 'webshot2'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nat.Rcheck/00install.out’ for details.
Packages required but not available: 'caret', 'Rglpk'

Package suggested but not available for checking: ‘gurobi’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'raster', 'leaflet', 'leaflet.extras', 'vegan', 'fasterize'

Packages suggested but not available for checking:
  'tm', 'rgeos', 'rgdal', 'maptools'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/NatureSounds.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘DEXSeq’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/NBBttest.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rrpack', 'glmnet', 'mpath'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘sSeq’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/NBLDA.Rcheck/00install.out’ for details.
Package required but not available: ‘magicaxis’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
NB.estimator: no visible global function definition for ‘optimize’
NB.estimator: no visible global function definition for ‘uniroot’
NB.example.dataset: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  optimize uniroot write.table
Consider adding
  importFrom("stats", "optimize", "uniroot")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘sample_data.txt’
Package required but not available: ‘caret’

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

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

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

Package suggested but not available for checking: ‘Hmisc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'quantreg', 'doParallel', 'plotly'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
ncbit : FUN: no visible global function definition for ‘read.table’
ncbit : FUN: no visible global function definition for ‘head’
Undefined global functions or variables:
  head read.table
Consider adding
  importFrom("utils", "head", "read.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
d0: no visible global function definition for ‘qnorm’
dncgamma: no visible global function definition for ‘dpois’
indncgamma: no visible global function definition for ‘pgamma’
indncgamma: no visible global function definition for ‘dpois’
inxncgamma: no visible global function definition for ‘qnorm’
inxncgamma: no visible global function definition for ‘pgamma’
inxncgamma: no visible global function definition for ‘dpois’
pncgamma: no visible global function definition for ‘pgamma’
pncgamma: no visible global function definition for ‘dpois’
Undefined global functions or variables:
  dpois pgamma qnorm
Consider adding
  importFrom("stats", "dpois", "pgamma", "qnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nCopula.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'plotly', 'ggrepel'
Error(s) in re-building vignettes:
  ...
--- re-building ‘nCov2019.Rmd’ using rmarkdown
Warning: Ignoring unknown aesthetics: x, y
Warning: Ignoring unknown aesthetics: x, y
Warning in pal_name(palette, type) : Unknown palette Green
Warning in log(diff + 1) : NaNs produced
Warning in log(diff + 1) : NaNs produced
Warning: Ignoring unknown aesthetics: x, y
Warning: Transformation introduced infinite values in discrete y-axis
Quitting from lines 259-280 (nCov2019.Rmd) 
Error: processing vignette ‘nCov2019.Rmd’ failed with diagnostics:
there is no package called 'ggrepel'
--- failed re-building ‘nCov2019.Rmd’

SUMMARY: processing the following file failed:
  ‘nCov2019.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  're2r', 'cdata', 'R.utils'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/NCSCopula.Rcheck/00install.out’ for details.
Packages required but not available: 'glmnet', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ashr’
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'networkDynamic', 'sna'

Packages suggested but not available for checking: 'tergm', 'tsna'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'AER', 'lmtest', 'mlogit'
Error(s) in re-building vignettes:
  ...
--- re-building ‘ndvtest.Rmd’ using rmarkdown
Quitting from lines 489-494 (ndvtest.Rmd) 
Error: processing vignette ‘ndvtest.Rmd’ failed with diagnostics:
there is no package called 'AER'
--- failed re-building ‘ndvtest.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'heatmaply', 'ConsensusClusterPlus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'viridis', 'fBasics', 'MBESS', 'car', 'ez', 'BayesFactor', 'ggpubr'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
Package required but not available: ‘msm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/NegBinBetaBinreg.Rcheck/00install.out’ for details.
Packages required but not available: 'DescTools', 'WRS2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'optimbase', 'optimsimplex'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'neonUtilities', 'R.utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'duckdb', 'R.utils', 'vroom'

Package suggested but not available for checking: ‘neonUtilities’

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

Package suggested but not available for checking: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'analogue', 'leaflet'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package required but not available: ‘graph’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Package required but not available: ‘sna’

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

Package suggested but not available for checking: ‘magic’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'expm', 'vegan', 'doParallel', 'ggfortify', 'ggraph'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pcalg', 'ppcor'

Package suggested but not available for checking: ‘furrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sna', 'networkDynamic'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'doParallel', 'ggraph', 'picante', 'Rfast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/netgen.Rcheck/00install.out’ for details.
Packages required but not available:
  'AnnotationDbi', 'genefilter', 'graph', 'graphite', 'glmnet',
  'org.Hs.eg.db', 'RCy3'

Package suggested but not available for checking: ‘ndexr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RBGL', 'tmvtnorm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘LIM’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/NetIndices.Rcheck/00install.out’ for details.
Package required but not available: ‘brainGraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'raster', 'CircStats', 'quickPlot', 'SpaDES.tools', 'rgeos'

Packages suggested but not available for checking: 'fastshp', 'SpaDES.core'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggnetwork', 'sna'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'meta', 'magic', 'metafor'

Package suggested but not available for checking: ‘hasseDiagram’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'readr', 'seqinr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ergm’
Package required but not available: ‘Hmisc’

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

Package suggested but not available for checking: ‘ggraph’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rfast', 'BiRewire'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DiagrammeR', 'segmented'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/NetSwan.Rcheck/00install.out’ for details.
Package required but not available: ‘sna’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'MCMCpack', 'Rmpfr', 'qgraph', 'ggrepel', 'GGally'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'qgraph', 'IsingFit', 'IsingSampler'

Package suggested but not available for checking: ‘networktools’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/networkDynamic.Rcheck/00install.out’ for details.
Package required but not available: ‘sna’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘map.png’ ‘maze.html’
Package required but not available: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘sna’
Error(s) in re-building vignettes:
  ...
--- re-building ‘networkVignette.Rnw’ using Sweave

‘network’ 1.17.1 (2021-06-12), part of the Statnet Project
* ‘news(package="network")’ for changes since last version
* ‘citation("network")’ for citation information
* ‘https://statnet.org’ for help, support, and other information


Error: processing vignette ‘networkVignette.Rnw’ failed with diagnostics:
 chunk 29 
Error in library(sna) : there is no package called ‘sna’

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

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘surveybootstrap’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/networksis.Rcheck/00install.out’ for details.
Package required but not available: ‘Rglpk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'R.matlab', 'qgraph', 'ppcor', 'doParallel', 'IsingFit'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'qgraph', 'IsingFit', 'NetworkComparisonTest', 'R.utils', 'smacof',
  'wordcloud'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'partykit', 'qgraph'

Packages suggested but not available for checking: 'R.rsp', 'fxregime'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'caret', 'RSNNS'
Malformed Description field: should contain one or more complete sentences.
mlptrain : rect: no visible global function definition for ‘polygon’
mlptrain : drawnet: no visible global function definition for ‘title’
mlptrain : drawnet: no visible global function definition for ‘polygon’
mlptrain : drawnet: no visible global function definition for ‘text’
mlptrain : drawnet: no visible global function definition for ‘lines’
mlptrain: no visible global function definition for ‘runif’
mlptrain: no visible global function definition for ‘locator’
mlptrain: no visible global function definition for ‘polygon’
mlptrain: no visible global function definition for ‘text’
rbftrain : rect: no visible global function definition for ‘polygon’
rbftrain : drawnet: no visible global function definition for ‘title’
rbftrain : drawnet: no visible global function definition for ‘polygon’
rbftrain : drawnet: no visible global function definition for ‘text’
rbftrain : drawnet: no visible global function definition for ‘lines’
rbftrain : graph: no visible global function definition for ‘title’
rbftrain : graph: no visible global function definition for ‘polygon’
rbftrain : graph: no visible global function definition for ‘text’
rbftrain : graph: no visible global function definition for ‘lines’
rbftrain : graph: no visible global function definition for ‘points’
rbftrain: no visible global function definition for ‘runif’
rbftrain: no visible global function definition for ‘locator’
rbftrain: no visible global function definition for ‘polygon’
rbftrain: no visible global function definition for ‘text’
rbftrain: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  kmeans lines locator points polygon runif text title
Consider adding
  importFrom("graphics", "lines", "locator", "points", "polygon", "text",
             "title")
  importFrom("stats", "kmeans", "runif")
to your NAMESPACE file.
Packages required but not available: 'caret', 'Hmisc', 'ggforce'

Packages suggested but not available for checking: 'RSNNS', 'plotly'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/neuRosim.Rcheck/00install.out’ for details.
Package required but not available: ‘ggpmisc’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Newdistns.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/newFocus.Rcheck/00install.out’ for details.
Package required but not available: ‘devtools’

Packages suggested but not available for checking: 'robotstxt', 'textdata'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nFactors.Rcheck/00install.out’ for details.
nfca : nFCAmain: no visible global function definition for ‘hist’
nfca : nFCAmain: no visible global function definition for
  ‘flush.console’
nfca : nFCAmain: no visible global function definition for ‘qnorm’
nfca : nFCAmain: no visible global function definition for ‘read.csv’
nfca : nFCAmain: no visible global function definition for ‘cor’
nfca : nFCAmain: no visible global function definition for ‘as.dist’
nfca : nFCAmain: no visible global function definition for ‘cophenetic’
nfca : nFCAmain: no visible global function definition for ‘hclust’
nfca : thresholdTEST: no visible global function definition for
  ‘read.csv’
nfca : gScript: no visible global function definition for ‘read.csv’
nfca : gScript0: no visible global function definition for ‘read.csv’
nfca : gMatrix: no visible global function definition for ‘read.csv’
nfca: no visible global function definition for ‘cor’
Undefined global functions or variables:
  as.dist cophenetic cor flush.console hclust hist qnorm read.csv
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cophenetic", "cor", "hclust", "qnorm")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘Hgraph.dot’ ‘Igraph.dot’
Package required but not available: ‘nflfastR’

Package suggested but not available for checking: ‘tidyverse’

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

Package suggested but not available for checking: ‘RSQLite’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'furrr', 'gsubfn', 'readr'

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'nfl4th', 'nflfastR', 'nflseedR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'graph', 'KEGGgraph'

Packages suggested but not available for checking: 'graphite', 'NFPdata'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nftbart.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘forecast’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ngspatial.Rcheck/00install.out’ for details.
Packages required but not available: 'fields', 'car'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mosaic’
Packages required but not available: 'R.utils', 'rosm', 'dataRetrieval'

Packages suggested but not available for checking:
  'ggmap', 'devtools', 'leaflet'

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

Packages suggested but not available for checking: 'wikilake', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘RSQLite’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'msm', 'MCMCpack'

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

Package suggested but not available for checking: ‘msm’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'caret', 'readr', 'rsample', 'lme4', 'lmtest', 'ggrepel', 'synthpop'
Error(s) in re-building vignettes:
  ...
--- re-building ‘LOS_model.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 163-172 (LOS_model.Rmd) 
Error: processing vignette ‘LOS_model.Rmd’ failed with diagnostics:
there is no package called 'lmtest'
--- failed re-building ‘LOS_model.Rmd’

--- re-building ‘ae_attendances.Rmd’ using rmarkdown
Quitting from lines 47-69 (ae_attendances.Rmd) 
Error: processing vignette ‘ae_attendances.Rmd’ failed with diagnostics:
there is no package called 'ggrepel'
--- failed re-building ‘ae_attendances.Rmd’

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

--- re-building ‘stranded_model.Rmd’ using rmarkdown
Quitting from lines 36-46 (stranded_model.Rmd) 
Error: processing vignette ‘stranded_model.Rmd’ failed with diagnostics:
there is no package called 'caret'
--- failed re-building ‘stranded_model.Rmd’

--- re-building ‘synthetic_news_data.Rmd’ using rmarkdown
Quitting from lines 50-57 (synthetic_news_data.Rmd) 
Error: processing vignette ‘synthetic_news_data.Rmd’ failed with diagnostics:
there is no package called 'readr'
--- failed re-building ‘synthetic_news_data.Rmd’

SUMMARY: processing the following files failed:
  ‘LOS_model.Rmd’ ‘ae_attendances.Rmd’ ‘stranded_model.Rmd’
  ‘synthetic_news_data.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dismo', 'raster', 'spider', 'vegan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'castor', 'geiger', 'raster', 'rgdal', 'rgeos'

Package suggested but not available for checking: ‘phytools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyverse’
Error(s) in re-building vignettes:
  ...
--- re-building ‘color-palette-demo.Rmd’ using rmarkdown
Quitting from lines 20-24 (color-palette-demo.Rmd) 
Error: processing vignette ‘color-palette-demo.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘color-palette-demo.Rmd’

SUMMARY: processing the following file failed:
  ‘color-palette-demo.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/NightDay.Rcheck/00install.out’ for details.
Packages required but not available: 'raster', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plotly', 'bipartite', 'bnstruct', 'fpc', 'missMDA', 'softImpute'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nimbleAPT.Rcheck/00install.out’ for details.
Packages required but not available: 'rcarbon', 'doSNOW'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nimbleEcology.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nimbleSCR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nimbleSMC.Rcheck/00install.out’ for details.
Package required but not available: ‘bbw’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages which this enhances but not available for checking:
  'estatapi', 'jpndistrict', 'jpmesh'
Packages required but not available: 'Rsamtools', 'S4Vectors'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/NIRStat.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Packages required but not available: 'fdasrvf', 'fda', 'fda.usc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nitrcbot.Rcheck/00install.out’ for details.
Package required but not available: ‘car’

Package suggested but not available for checking: ‘rsq’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/NlcOptim.Rcheck/00install.out’ for details.
Packages required but not available:
  'a4Core', 'MLInterfaces', 'Biobase', 'multtest', 'pamr', 'ipred'

Package suggested but not available for checking: ‘ALL’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nlmeODE.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘Hmisc’
Malformed Title field: should not end in a period.
Pwr.lme: no visible global function definition for ‘anova’
Pwr.lme: no visible global function definition for ‘qf’
Pwr.lme: no visible global function definition for ‘pf’
logLik1.lme: no visible global function definition for ‘coef’
logLik1.lme: no visible global function definition for ‘model.matrix’
logLik1.lme: no visible global function definition for ‘predict’
logLik1.lme: no visible global function definition for ‘formula’
runScript: no visible binding for global variable ‘example’
sigmaTolme: no visible global function definition for ‘vcov’
simulateY.lme: no visible global function definition for ‘runif’
simulateY.lme: no visible global function definition for ‘fitted’
simulateY.lme: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  anova coef example fitted formula model.matrix pf predict qf rnorm
  runif vcov
Consider adding
  importFrom("stats", "anova", "coef", "fitted", "formula",
             "model.matrix", "pf", "predict", "qf", "rnorm", "runif",
             "vcov")
  importFrom("utils", "example")
to your NAMESPACE file.
checkRd: (7) nlmeU-package.Rd:15-16: invalid email address: Tomasz Burzykowski  <tomasz.burzykowski@uhasselt.be>
Packages required but not available: 'Hmisc', 'quantreg'

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

Packages suggested but not available for checking:
  'broom.mixed', 'devtools', 'dotwhisker', 'expm', 'madness', 'vpc',
  'xgxr', 'xpose', 'forecast', 'latticeExtra'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'coin', 'earth'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'SuperLearner', 'bde', 'np'

Package suggested but not available for checking: ‘glmnet’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'car', 'nls2', 'segmented'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Bootstrapping.Rmd’ using rmarkdown
Quitting from lines 21-25 (Bootstrapping.Rmd) 
Error: processing vignette ‘Bootstrapping.Rmd’ failed with diagnostics:
there is no package called 'car'
--- failed re-building ‘Bootstrapping.Rmd’

--- re-building ‘Confidence-Bands.Rmd’ using rmarkdown
--- finished re-building ‘Confidence-Bands.Rmd’

--- re-building ‘Models-and-Functions.Rmd’ using rmarkdown
--- finished re-building ‘Models-and-Functions.Rmd’

--- re-building ‘nlraa-AgronJ-paper.Rmd’ using rmarkdown
--- finished re-building ‘nlraa-AgronJ-paper.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'cond', 'csampling', 'marg'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nlreg.Rcheck/00install.out’ for details.
Packages required but not available: 'rms', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'furrr', 'raster', 'EasyABC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nls2.Rcheck/00install.out’ for details.
Packages required but not available: 'orthopolynom', 'gaussquad'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nlsic.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nlsMicrobio.Rcheck/00install.out’ for details.
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nltm.Rcheck/00install.out’ for details.
Packages required but not available: 'EbayesThresh', 'adlift'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nlts.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'DDD', 'Hmisc', 'TESS', 'TreeSim', 'DAISIE'
Error(s) in re-building vignettes:
  ...
--- re-building ‘get_nltt_values.Rmd’ using rmarkdown
--- finished re-building ‘get_nltt_values.Rmd’

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

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

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

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

--- re-building ‘walkthrough.Rmd’ using rmarkdown
Quitting from lines 19-27 (walkthrough.Rmd) 
Error: processing vignette ‘walkthrough.Rmd’ failed with diagnostics:
there is no package called 'TESS'
--- failed re-building ‘walkthrough.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘devtools’

Package suggested but not available for checking: ‘netmeta’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rjags', 'ks', 'MCMCpack'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘INLA’
Packages required but not available: 'netmeta', 'meta'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'meta', 'netmeta'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
nnmf_als: no visible global function definition for ‘rnorm’
nnmf_mm: no visible global function definition for ‘rnorm’
nnmf_prob: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Packages required but not available: 'pkgmaker', 'doParallel', 'Biobase'

Packages suggested but not available for checking: 'doMPI', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘unmarked’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'systemfit', 'maxLik', 'AER', 'mlogit', 'Hmisc', 'gsubfn'

Package suggested but not available for checking: ‘recipes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rglpk’
Error(s) in re-building vignettes:
  ...
--- re-building ‘An_overview.Rnw’ using Sweave
found several files...
--- finished re-building ‘An_overview.Rnw’

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

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

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

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

--- re-building ‘TAportfolio.Rnw’ using Sweave
Error in solve.QP(Dmat = covMatrix, dvec = rep(0, na), Amat = t(rbind(A,  : 
  matrix D in quadratic function is not positive definite!
--- finished re-building ‘TAportfolio.Rnw’

--- re-building ‘portfolio.Rnw’ using Sweave
Loading required namespace: Rglpk
Failed with error:  'there is no package called 'Rglpk''

Error: processing vignette ‘portfolio.Rnw’ failed with diagnostics:
 chunk 14 
Error in minCVaR(R, q = 0.1) : package 'Rglpk'

--- failed re-building 'portfolio.Rnw'

--- re-building 'qTableEx.Rnw' using Sweave
--- finished re-building 'qTableEx.Rnw'

--- re-building 'repair.Rnw' using Sweave
--- finished re-building 'repair.Rnw'

--- re-building 'vectorise.Rnw' using Sweave
--- finished re-building 'vectorise.Rnw'

SUMMARY: processing the following file failed:
  'portfolio.Rnw'

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘dygraphs’

Packages suggested but not available for checking:
  'xpose', 'pmxTools', 'Hmisc', 'rsample', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nmw.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘brnn’
Running examples in ‘NNbenchmark-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: NNtrainPredict
> ### Title: Generic Functions for Training and Predicting
> ### Aliases: NNtrainPredict trainPredict_1mth1data trainPredict_1data
> ###   trainPredict_1pkg
> 
> ### ** Examples
> 
> nrep <- 2       
> odir <- tempdir()
> 
> ### Package with one method/optimization algorithm
> library("brnn")
Error in library("brnn") : there is no package called ‘brnn’
Execution halted
Packages required but not available: 'forecast', 'glmnet', 'tsutils'

Package suggested but not available for checking: ‘thief’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'RPostgreSQL', 'stars'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nngeo.Rcheck/00install.out’ for details.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'doParallel', 'caret', 'dtw', 'dynlm', 'meboot', 'Quandl', 'Rfast',
  'tseries'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fields', 'tagcloud'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survRM2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'mlr', 'mlrCPO'
Error(s) in re-building vignettes:
  ...
--- re-building ‘nntrf.Rmd’ using rmarkdown
--- finished re-building ‘nntrf.Rmd’

--- re-building ‘nntrf_regresion.Rmd’ using rmarkdown
Quitting from lines 21-25 (nntrf_regresion.Rmd) 
Error: processing vignette ‘nntrf_regresion.Rmd’ failed with diagnostics:
there is no package called 'mlr'
--- failed re-building ‘nntrf_regresion.Rmd’

--- re-building ‘nntrf_tuning.Rmd’ using rmarkdown
Quitting from lines 20-24 (nntrf_tuning.Rmd) 
Error: processing vignette ‘nntrf_tuning.Rmd’ failed with diagnostics:
there is no package called 'mlr'
--- failed re-building ‘nntrf_tuning.Rmd’

SUMMARY: processing the following files failed:
  ‘nntrf_regresion.Rmd’ ‘nntrf_tuning.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'httptest', 'mapdata'
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting_started.Rmd’ using rmarkdown
Quitting from lines 13-16 (getting_started.Rmd) 
Error: processing vignette ‘getting_started.Rmd’ failed with diagnostics:
there is no package called 'httptest'
--- failed re-building ‘getting_started.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'choroplethr', 'hurricaneexposure', 'viridis'

Package suggested but not available for checking: ‘hurricaneexposuredata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘rjags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'arrow', 'bit64', 'readr', 'vroom'
Running examples in ‘noctua-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: noctua_options
> ### Title: A method to configure noctua backend options.
> ### Aliases: noctua_options
> 
> ### ** Examples
> 
> library(noctua)
> 
> # change file parser from default data.table to vroom
> noctua_options("vroom")
Error: Please install vroom package and try again
Execution halted
Packages required but not available: 'RSQLite', 'RPostgres'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
makeRules: no visible global function definition for ‘sd’
makeRules: no visible global function definition for ‘rnorm’
nodeHarvest: no visible global function definition for ‘capture.output’
nodeHarvest: no visible global function definition for ‘lm’
nodeHarvest: no visible global function definition for ‘coef’
plot.nodeHarvest: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  capture.output coef lm rgb rnorm sd
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "coef", "lm", "rnorm", "sd")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Packages required but not available:
  'RPANDA', 'apTreeshape', 'phangorn', 'DDD', 'Rmpfr', 'phylobase',
  'geiger', 'babette', 'beautier', 'beastier', 'mauricer'

Packages suggested but not available for checking: 'phytools', 'TreeSim'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'picante', 'raster', 'vegan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'IRanges', 'GenomicRanges', 'Rsamtools', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nomclust.Rcheck/00install.out’ for details.
Package required but not available: ‘mirt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘readr’
Package required but not available: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rms', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘MCMCpack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'glmnet', 'tidyverse'

Package suggested but not available for checking: ‘ClusterR’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'tsDyn'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'mirt', 'AER', 'faraway', 'mlogit'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Hmisc', 'rms', 'geometry'

Depends: includes the non-default packages:
  'lpSolve', 'gdata', 'Hmisc', 'rms', 'geometry', 'psych', 'pwt'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘doParallel’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'metafor', 'MCMCglmm'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'odbc', 'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/NormalGamma.Rcheck/00install.out’ for details.
Package required but not available: ‘rio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/NORMA.Rcheck/00install.out’ for details.
Package required but not available: ‘lcmm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
ajb.norm.test: no visible global function definition for ‘rnorm’
frosini.norm.test: no visible global function definition for ‘var’
frosini.norm.test: no visible global function definition for ‘pnorm’
frosini.norm.test: no visible global function definition for ‘rnorm’
geary.norm.test: no visible global function definition for ‘rnorm’
hegazy1.norm.test: no visible global function definition for ‘var’
hegazy1.norm.test: no visible global function definition for ‘qnorm’
hegazy1.norm.test: no visible global function definition for ‘rnorm’
hegazy2.norm.test: no visible global function definition for ‘var’
hegazy2.norm.test: no visible global function definition for ‘qnorm’
hegazy2.norm.test: no visible global function definition for ‘rnorm’
jb.norm.test: no visible global function definition for ‘rnorm’
kurtosis.norm.test: no visible global function definition for ‘rnorm’
skewness.norm.test: no visible global function definition for ‘rnorm’
spiegelhalter.norm.test: no visible global function definition for
  ‘rnorm’
wb.norm.test: no visible global function definition for ‘qnorm’
wb.norm.test: no visible global function definition for ‘var’
wb.norm.test: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  pnorm qnorm rnorm var
Consider adding
  importFrom("stats", "pnorm", "qnorm", "rnorm", "var")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nortestARMA.Rcheck/00install.out’ for details.
Packages required but not available: 'forecast', 'tseries'

Package suggested but not available for checking: ‘ggfortify’

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

Packages suggested but not available for checking:
  'tidyverse', 'ggnetwork', 'viridis', 'gganimate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/NostalgiR.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/notifyR.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘brms’
Running examples in ‘novelforestSG-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: download_model
> ### Title: Download Model Fitted to the 'novelforest' Data
> ### Aliases: download_model
> 
> ### ** Examples
> 
> novelforest_model <- download_model()
To save the model locally, use argument save_to = 'path/filename.rds'
Downloading model (size: 16.5 Mb)
> 
> # library(brms)  # recommended
> summary(novelforest_model)
Loading required package: rstan
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘rstan’
Error in .requirePackage(package) : 
  unable to find required package ‘rstan’
Calls: summary ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nowcastDFM.Rcheck/00install.out’ for details.
Packages required but not available: 'xts', 'magic', 'RMySQL', 'vars'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
.newReportId : <anonymous>: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package required but not available: ‘multcomp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nparLD.Rcheck/00install.out’ for details.
Package required but not available: ‘TH.data’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/NPBayesImputeCat.Rcheck/00install.out’ for details.
Packages required but not available: 'Benchmarking', 'np', 'Rglpk'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/NPCD.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/NPCirc.Rcheck/00install.out’ for details.
Package required but not available: ‘coin’

Package suggested but not available for checking: ‘car’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'doParallel', 'itertools'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/NPflow.Rcheck/00install.out’ for details.
Package required but not available: ‘smcure’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘styler’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ez’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'R.utils', 'spatstat', 'FDRreg', 'REBayes', 'CAMAN', 'Hmisc',
  'mosaic'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'ks', 'rgdal'

Package suggested but not available for checking: ‘rgeos’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘SPEI’
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'ada'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘snowFT’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/npsf.Rcheck/00install.out’ for details.
nps.test: no visible global function definition for ‘qnorm’
nps.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
‘library’ or ‘require’ call to ‘parallel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
npst: no visible global function definition for ‘mclapply’
Undefined global functions or variables:
  mclapply
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/npsurv.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘tidyverse’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic_functionalities.Rmd’ using rmarkdown
--- finished re-building ‘basic_functionalities.Rmd’

--- re-building ‘example1.Rmd’ using rmarkdown
Quitting from lines 22-25 (example1.Rmd) 
Error: processing vignette ‘example1.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘example1.Rmd’

--- re-building ‘example2.Rmd’ using rmarkdown
Quitting from lines 22-25 (example2.Rmd) 
Error: processing vignette ‘example2.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘example2.Rmd’

SUMMARY: processing the following files failed:
  ‘example1.Rmd’ ‘example2.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nricens.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'CCA', 'glmnet'
Package suggested but not available for checking: ‘httptest’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(httptest)
  Error in library(httptest) : there is no package called 'httptest'
  Execution halted
Package required but not available: ‘np’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nsga2R.Rcheck/00install.out’ for details.
Package required but not available: ‘mlr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘NSM3’
Packages required but not available:
  'agricolae', 'BSDA', 'coin', 'Hmisc', 'metafor', 'np', 'quantreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nspmix.Rcheck/00install.out’ for details.
Package required but not available: ‘sde’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘readr’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘MCMCpack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘fields’

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fpc', 'forecast', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pedtools', 'ribd'

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
'LazyData' is specified without a 'data' directory
Package required but not available: ‘tmvtnorm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘qrng’

Packages suggested but not available for checking: 'qrmdata', 'xts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'GGally', 'mapproj'
Error(s) in re-building vignettes:
  ...
--- re-building ‘README.Rmd’ using rmarkdown
Quitting from lines 64-82 (README.Rmd) 
Error: processing vignette ‘README.Rmd’ failed with diagnostics:
there is no package called 'GGally'
--- failed re-building ‘README.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘devtools’
Packages suggested but not available for checking: 'tigris', 'socialmixr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘o2geosocial.Rmd’ using rmarkdown
Registered S3 methods overwritten by 'o2geosocial':
  method                    from       
  plot.outbreaker_chains    outbreaker2
  print.custom_likelihoods  outbreaker2
  print.custom_priors       outbreaker2
  print.outbreaker_chains   outbreaker2
  summary.outbreaker_chains outbreaker2
Quitting from lines 152-165 (o2geosocial.Rmd) 
Error: processing vignette ‘o2geosocial.Rmd’ failed with diagnostics:
there is no package called 'socialmixr'
--- failed re-building ‘o2geosocial.Rmd’

SUMMARY: processing the following file failed:
  ‘o2geosocial.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RSQLite’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/oaPlots.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rgdal', 'rgeos', 'spdep', 'seg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'modeest', 'truncdist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rfast', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/objectProperties.Rcheck/00install.out’ for details.
Package required but not available: ‘mda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'pec', 'missForest', 'glmnet', 'prodlim'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
IBMD: no visible global function definition for ‘runif’
IBMD: no visible global function definition for ‘quantile’
RAI: no visible global function definition for ‘runif’
RAI: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile runif
Consider adding
  importFrom("stats", "quantile", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'BIEN', 'taxize', 'leaflet', 'RPostgreSQL', 'viridis', 'waffle'

Package suggested but not available for checking: ‘bit64’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rgdal', 'rgeos', 'spData'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'leaflet', 'leaflet.extras', 'mapview'

Package suggested but not available for checking: ‘rio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'mapdata', 'raster', 'fields', 'maptools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plot3Drgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘oce’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/oceanwaves.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'automap', 'marmap', 'raster', 'rgeos', 'RSQLite', 'R.utils'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/oce.Rcheck/00install.out’ for details.
Package required but not available: ‘flexclust’

Package suggested but not available for checking: ‘seriation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'fields', 'SSN', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ocomposition.Rcheck/00install.out’ for details.
Package required but not available: ‘bit64’

Package suggested but not available for checking: ‘RSQLite’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'tidymodels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ks', 'mvtsplot'

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘morse’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ODEnetwork.Rcheck/00install.out’ for details.
Package required but not available: ‘ODEnetwork’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/oem.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘forestplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘maxLik’

Packages suggested but not available for checking: 'glmx', 'lmtest'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ICS', 'ICSNP'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyverse’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘ojsr-vignette.Rmd’ using rmarkdown
Quitting from lines 52-72 (ojsr-vignette.Rmd) 
Error: processing vignette ‘ojsr-vignette.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘ojsr-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
avgokmts: no visible global function definition for ‘aggregate’
downloadstn: no visible global function definition for ‘read.csv’
nearstn: no visible binding for global variable ‘okstations’
nearstn: no visible binding for global variable ‘Commissioned’
nearstn: no visible binding for global variable ‘Decommissioned’
okcurobs: no visible global function definition for ‘read.csv’
okmts: no visible binding for global variable ‘okstations’
okmts: no visible binding for global variable ‘TIME’
retrievemts: no visible global function definition for ‘read.csv’
totalprecip: no visible binding for global variable ‘TIME’
totalprecip: no visible global function definition for ‘aggregate’
vincenty: no visible global function definition for ‘runif’
Undefined global functions or variables:
  Commissioned Decommissioned TIME aggregate okstations read.csv runif
Consider adding
  importFrom("stats", "aggregate", "runif")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Packages required but not available:
  'car', 'ggpubr', 'ggrepel', 'lme4', 'lmerTest'

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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/OLScurve.Rcheck/00install.out’ for details.
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
fhcor: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor
Consider adding
  importFrom("stats", "cor")
to your NAMESPACE file.
Packages required but not available: 'plotly', 'dendextend', 'STRINGdb'

Package suggested but not available for checking: ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'irlba'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ff', 'glmnet'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ROI.plugin.glpk’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(magrittr)
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  > library(ROI)
  ROI: R Optimization Infrastructure
  Registered solver plugins: nlminb.
  Default solver: auto.
  > library(ROI.plugin.glpk)
  Error in library(ROI.plugin.glpk) : 
    there is no package called 'ROI.plugin.glpk'
  Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'KEGGREST', 'ggfortify'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Error(s) in re-building vignettes:
  ...
--- re-building ‘RoeDeerMass-simulation.Rnw’ using Sweave

Error: processing vignette ‘RoeDeerMass-simulation.Rnw’ failed with diagnostics:
 chunk 6 (label = testTF) 
Error in loadNamespace(x) : there is no package called ‘lme4’

--- failed re-building ‘RoeDeerMass-simulation.Rnw’

SUMMARY: processing the following file failed:
  ‘RoeDeerMass-simulation.Rnw’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘rstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'glmnet', 'sva', 'GenomicFeatures', 'genefilter', 'tidyverse',
  'GenomicRanges', 'IRanges', 'S4Vectors', 'org.Hs.eg.db',
  'TxDb.Hsapiens.UCSC.hg19.knownGene'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Oncotree.Rcheck/00install.out’ for details.
Packages required but not available: 'caret', 'readr', 'pdp'

Package suggested but not available for checking: ‘devtools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘genlasso’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘oneclust.Rmd’ using rmarkdown
Quitting from lines 193-194 (oneclust.Rmd) 
Error: processing vignette ‘oneclust.Rmd’ failed with diagnostics:
there is no package called 'genlasso'
--- failed re-building ‘oneclust.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'plotly', 'smacof', 'ggpubr', 'dendextend', 'vcfR'

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

Package suggested but not available for checking: ‘rgdal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gmm', 'ivreg', 'lmtest', 'msm'

Packages suggested but not available for checking:
  'AER', 'haven', 'ivtools', 'lfe'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ONETr.Rcheck/00install.out’ for details.
Package required but not available: ‘car’

Package suggested but not available for checking: ‘AID’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/onlinePCA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/onls.Rcheck/00install.out’ for details.
Packages required but not available:
  'spatstat.core', 'spatstat.geom', 'spatstat.random'

Package suggested but not available for checking: ‘spatstat’

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

Package suggested but not available for checking: ‘vroom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ontoFAST.Rcheck/00install.out’ for details.
Package required but not available: ‘Rgraphviz’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'keyATM', 'irr'

Packages suggested but not available for checking:
  'text2vec', 'topicmodels', 'stm', 'seededlda', 'quanteda.textmodels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
ci.prop: no visible global function definition for ‘qf’
ci.prop: no visible global function definition for ‘qnorm’
ePCP: no visible global function definition for ‘qnorm’
sevennum: no visible global function definition for ‘na.omit’
sevennum: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  na.omit qf qnorm quantile
Consider adding
  importFrom("stats", "na.omit", "qf", "qnorm", "quantile")
to your NAMESPACE file.
Package suggested but not available for checking: ‘devtools’
Packages required but not available:
  'caret', 'forecast', 'furrr', 'glmnet', 'imputeTS', 'lmtest', 'vars',
  'xts'

Package suggested but not available for checking: ‘quantmod’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'benchmarkme', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'orthopolynom', 'crossdes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'maptools'

Package suggested but not available for checking: ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'latticeExtra', 'mapproj'

Packages suggested but not available for checking: 'mapdata', 'quantreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘bibliometrix’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/openblender.Rcheck/00install.out’ for details.
Skipping vignette re-building
Packages suggested but not available for checking:
  'arrow', 'haven', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Package required but not available: ‘secr’

Packages suggested but not available for checking:
  'RMark', 'rgdal', 'R2ucare'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘readr’

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

Package suggested but not available for checking: ‘tmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping vignette re-building
Packages suggested but not available for checking: 'mlr', 'farff', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'MSEtool', 'DLMtool', 'SAMtool'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'snowfall', 'lme4', 'umx', 'ifaTools'
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘openNLPmodels.en’
Package required but not available: ‘tidyverse’

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

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

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘jose’
Error(s) in re-building vignettes:
  ...
--- re-building ‘bignum.Rmd’ using rmarkdown
--- finished re-building ‘bignum.Rmd’

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

--- re-building ‘keys.Rmd’ using rmarkdown
Quitting from lines 88-91 (keys.Rmd) 
Error: processing vignette ‘keys.Rmd’ failed with diagnostics:
there is no package called 'jose'
--- failed re-building ‘keys.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'rgrass7', 'rgdal', 'raster', 'SSN'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'rgdal'

Package suggested but not available for checking: ‘maptools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'maptools', 'openair', 'raster', 'rgdal', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'raster', 'rgdal'
Package required but not available: ‘InSilicoVA’

Package suggested but not available for checking: ‘nbc4va’

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

Packages suggested but not available for checking: 'quantreg', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DistributionOptimization', 'mixtools', 'mixAK', 'multimode',
  'ClusterR', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'likert', 'tm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/optAUC.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/optbdmaeAT.Rcheck/00install.out’ for details.
Packages required but not available: 'ipred', 'msm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'Biobase', 'annotate', 'GO.db', 'org.At.tair.db'
Package unavailable to check Rd xrefs: ‘Biobase’
Packages required but not available: 'plotly', 'orthopolynom'

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/OptHoldoutSize.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'fpc', 'ggrepel'
Running examples in ‘opticskxi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggpairs
> ### Title: Plot multiple axes of a data frame or a fortified dimension
> ###   reduction.
> ### Aliases: ggpairs
> 
> ### ** Examples
> 
> df_pca <- fortify_pca(iris[-5])
> ggpairs(df_pca)
> df_pca <- fortify_pca(iris[-5], sup_vars = iris[5])
> ggpairs(df_pca, group = 'Species', ellipses = TRUE, variables = TRUE)
Error in loadNamespace(x) : there is no package called ‘ggrepel’
Calls: ggpairs ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [3s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(opticskxi)
  > 
  > test_check("opticskxi")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 6 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-optics_plots.R:16:1): (code run outside of `test_that()`) ───────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'fpc'
  Backtrace:
       ▆
    1. ├─opticskxi::opticskxi_pipeline(iris_scaled, kxi_prms) at test-optics_plots.R:16:0
    2. │ └─parallel::mclapply(...)
    3. │   └─base::lapply(X = X, FUN = FUN, ...)
    4. │     └─opticskxi FUN(X[[i]], ...)
    5. │       └─... %>% unlist
    6. ├─base::unlist(.)
    7. └─base::loadNamespace(x)
    8.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
    9.     └─base withOneRestart(expr, restarts[[1L]])
   10.       └─base doWithOneRestart(return(expr), restart)
  ── Error (test-opticskxi.R:5:1): (code run outside of `test_that()`) ───────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'fpc'
  Backtrace:
       ▆
    1. ├─opticskxi::opticskxi_pipeline(scale(iris[-5]), params) at test-opticskxi.R:5:0
    2. │ └─parallel::mclapply(...)
    3. │   └─base::lapply(X = X, FUN = FUN, ...)
    4. │     └─opticskxi FUN(X[[i]], ...)
    5. │       └─... %>% unlist
    6. ├─base::unlist(.)
    7. └─base::loadNamespace(x)
    8.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
    9.     └─base withOneRestart(expr, restarts[[1L]])
   10.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 6 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘opticskxi.Rnw’ using Sweave

Error: processing vignette ‘opticskxi.Rnw’ failed with diagnostics:
 chunk 7 (label = hla_metrics) 
Error in loadNamespace(x) : there is no package called 'fpc'

--- failed re-building 'opticskxi.Rnw'

SUMMARY: processing the following file failed:
  'opticskxi.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'betareg', 'mefa4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'DiagrammeR', 'survey'
Running examples in ‘optimall-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: multiwave_diagram
> ### Title: Print Summary Diagram of Multiwave Object
> ### Aliases: multiwave_diagram
> 
> ### ** Examples
> 
> MySurvey <- new_multiwave(phases = 2, waves = c(1, 3))
> multiwave_diagram(MySurvey)
Error: Please install DiagrammeR: install.packages('DiagrammeR').
         Otherwise, try 'summary()'
Execution halted
Running ‘testthat.R’ [80s/118s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(optimall)
  > 
  > test_check("optimall")
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 204 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On Linux (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-multiwave_diagram.R:38:3): multiwave_diagram works ──────────────
  Error: Please install DiagrammeR: install.packages('DiagrammeR').
           Otherwise, try 'summary()'
  Backtrace:
      ▆
   1. └─optimall::multiwave_diagram(MySurvey) at test-multiwave_diagram.R:38:2
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 204 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘GreedyExperimentalDesign’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DepthProc', 'fields', 'geometry'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/optimbase.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘quantreg’
Package required but not available: ‘randtoolbox’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/optimization.Rcheck/00install.out’ for details.
Packages required but not available: 'tidyverse', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Package required but not available: ‘optimbase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/optimStrat.Rcheck/00install.out’ for details.
checkRd: (7) Rcgmin.Rd:99-100: \item in \describe must have non-empty label
checkRd: (7) Rcgminb.Rd:56-57: \item in \describe must have non-empty label
checkRd: (7) Rcgminu.Rd:48-49: \item in \describe must have non-empty label
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/OptInterim.Rcheck/00install.out’ for details.
Packages required but not available: 'weights', 'Hmisc'

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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/optiscale.Rcheck/00install.out’ for details.
Packages required but not available:
  'kinship2', 'nadiv', 'pedigree', 'magic', 'doParallel', 'optiSolve'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyverse’
Package required but not available: ‘survey’

Packages suggested but not available for checking:
  'RItools', 'biglm', 'brglm', 'arm', 'rrelaxiv'

Packages which this enhances but not available for checking:
  'CBPS', 'haven'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/optrcdmaeAT.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/optrees.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘twang’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘arules’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ReIns', 'evmix'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘graph’
Agrestiind.CI: no visible global function definition for ‘qnorm’
BPexact.CI: no visible global function definition for ‘uniroot’
BPmidp.CI: no visible global function definition for ‘uniroot’
Cornfieldexact.CI: no visible global function definition for ‘uniroot’
Cornfieldmidp.CI: no visible global function definition for ‘uniroot’
Gart.CI: no visible global function definition for ‘qnorm’
Invsinh.CI: no visible global function definition for ‘qnorm’
Woolf.CI: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm uniroot
Consider adding
  importFrom("stats", "qnorm", "uniroot")
to your NAMESPACE file.
Packages required but not available: 'raster', 'latticeExtra', 'rgdal'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'faux', 'brms'

Packages suggested but not available for checking: 'haven', 'Hmisc'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ordDisp.Rcheck/00install.out’ for details.
Packages required but not available: 'Rfast', 'doRNG', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ORDER2PARENT.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/orderbook.Rcheck/00install.out’ for details.
Package required but not available: ‘RSQLite’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Newdistns', 'gamlss.dist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/OrdFacReg.Rcheck/00install.out’ for details.
Package required but not available: ‘vegan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DESeq2', 'SummarizedExperiment', 'devtools', 'dclone'

Package suggested but not available for checking: ‘Biobase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘caret’
Found the following significant warnings:
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:33: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ forming offset [176, 183] is out of the bounds [0, 176] of object ‘b’ with type ‘arma::vec’ {aka ‘arma::Col<double>’} [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ordinalClust.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ordinalClust.Rmd’ using rmarkdown

Attaching package: 'ordinalClust'

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

    plot

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

    plot, summary

`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning: Removed 14 rows containing missing values (geom_bar).
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Quitting from lines 270-289 (ordinalClust.Rmd) 
Error: processing vignette ‘ordinalClust.Rmd’ failed with diagnostics:
there is no package called 'caret'
--- failed re-building ‘ordinalClust.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ordinalCont.Rcheck/00install.out’ for details.
Package required but not available: ‘verification’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ordinalgmifs.Rcheck/00install.out’ for details.
Packages required but not available: 'mirt', 'NominalLogisticBiplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'glmnet', 'penalized', 'rms'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ordinalpattern.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘lme4’
Package required but not available: ‘rjags’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RLRsim', 'glmpath'

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

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
Package vignette with placeholder title ‘Vignette Title’:
  ‘intro.Rmd’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/orgR.Rcheck/00install.out’ for details.
ORICC1: no visible binding for global variable ‘sd’
ORICC1: no visible global function definition for ‘write.table’
ORICC1: no visible global function definition for ‘postscript’
ORICC1: no visible global function definition for ‘jpeg’
ORICC1: no visible global function definition for ‘points’
ORICC1: no visible global function definition for ‘dev.off’
ORICC1: no visible global function definition for ‘par’
ORICC2: no visible binding for global variable ‘sd’
ORICC2: no visible global function definition for ‘write.table’
ORICC2: no visible global function definition for ‘postscript’
ORICC2: no visible global function definition for ‘jpeg’
ORICC2: no visible global function definition for ‘points’
ORICC2: no visible global function definition for ‘dev.off’
ORICC2: no visible global function definition for ‘par’
Undefined global functions or variables:
  dev.off jpeg par points postscript sd write.table
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "postscript")
  importFrom("graphics", "par", "points")
  importFrom("stats", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘cluster of fitted mean data.eps’ ‘cluster of fitted mean data.txt’
  ‘cluster of raw data.txt’
Package required but not available: ‘future.apply’

Packages suggested but not available for checking: 'glmnet', 'forecast'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/orloca.Rcheck/00install.out’ for details.
Packages required but not available:
  'rms', 'Hmisc', 'doParallel', 'benchmarkme'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
mdr.c: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Package required but not available: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘fmri’
'LazyData' is specified without a 'data' directory
  'LazyDataCompression' is specified without a 'data' directory
Package required but not available: ‘msm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/orsifronts.Rcheck/00install.out’ for details.
Package required but not available: ‘dr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
plot.SplineBasis: no visible global function definition for ‘matplot’
plot,SplineBasis-matrix: no visible global function definition for
  ‘matplot’
plot,SplineBasis-missing: no visible global function definition for
  ‘matplot’
Undefined global functions or variables:
  matplot
Consider adding
  importFrom("graphics", "matplot")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/orthopolynom.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'tm', 'topicmodels', 'xlsx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mc2d’

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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/osmar.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘raster’
Packages required but not available:
  'geoR', 'mapview', 'nngeo', 'rgdal', 'splancs'

Packages suggested but not available for checking:
  'PrevMap', 'leafem', 'raster'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggm', 'mapproj', 'rgeos', 'spatstat', 'spatstat.core',
  'spatstat.geom'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mapsf’
Package required but not available: ‘R.utils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'hypervolume', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pec', 'prodlim'

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

Package suggested but not available for checking: ‘Rcplex’

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
Packages required but not available:
  'missMDA', 'FactoMineR', 'StatMatch', 'ROI.plugin.glpk', 'party',
  'vcd'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/OTRselect.Rcheck/00install.out’ for details.
Package required but not available: ‘plotly’

Package suggested but not available for checking: ‘stream’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'R.utils'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘geiger’
Package suggested but not available for checking: ‘epicontacts’
checkRd: (7) palettes.Rd:25: invalid email address: thibautjombart@gmail_com
Package required but not available: ‘quantreg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'airt', 'EstCRM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'HDoutliers', 'FastPCS', 'cellWise', 'GGally', 'memisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/OutrankingTools.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘AER’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [4s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(outreg)
  > 
  > test_check("outreg")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 27 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_validfits.R:48:3): supported objects ────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `library(AER)`: there is no package called 'AER'
  Backtrace:
      ▆
   1. └─base::library(AER) at test_validfits.R:48:2
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 27 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘devtools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'geiger', 'phytools', 'paleotree', 'phangorn', 'phylolm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/overlapping.Rcheck/00install.out’ for details.
Package required but not available: ‘spatstat.geom’

Packages suggested but not available for checking: 'maptools', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘maptools’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggrepel', 'ggvenn'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'twang', 'Amelia', 'devtools', 'ggrepel', 'metR', 'survey'

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
Packages required but not available: 'readr', 'leaflet', 'ggrepel'

Packages suggested but not available for checking: 'showtext', 'plm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘leaflet’
Package required but not available: ‘rgdal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘httptest’
'LazyData' is specified without a 'data' directory
loadCSVtoP2distance: no visible global function definition for
  ‘read.table’
p2distance : calcularDistancia: no visible binding for global variable
  ‘sd’
p2distance : ordenarVariables: no visible global function definition
  for ‘cor’
p2distance : calculoFactoresPonderacion: no visible global function
  definition for ‘lm’
p2distance: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor lm read.table sd
Consider adding
  importFrom("stats", "cor", "lm", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/p3state.msm.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
pacbpred : thetaFunc: no visible global function definition for ‘lsfit’
pacbpred : thetaFunc: no visible global function definition for ‘rnorm’
pacbpred: no visible global function definition for ‘var’
pacbpred: no visible global function definition for ‘runif’
pacbpred: no visible global function definition for ‘rnorm’
pacbpred: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  lsfit rbinom rnorm runif var
Consider adding
  importFrom("stats", "lsfit", "rbinom", "rnorm", "runif", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'R.utils', 'sugrrants'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Running examples in ‘packager-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create
> ### Title: Create a Package Template
> ### Aliases: create
> 
> ### ** Examples
> 
> path <- file.path(tempdir(), "myFirstPackage")
> packager::create(path = path, fakemake = "roxygen2")
* Adding `.Rprofile` to /home/hornik/tmp/scratch/RtmpmqP36w/myFirstPackage/.gitignore
* Adding `*.tar.gz` to /home/hornik/tmp/scratch/RtmpmqP36w/myFirstPackage/.gitignore
* Adding `myFirstPackage.Rcheck` to /home/hornik/tmp/scratch/RtmpmqP36w/myFirstPackage/.gitignore
* Creating `Makefile` from template.
* Adding `Makefile` to `.Rbuildignore`.
Warning in update_description(path = path, title = tools::toTitleCase(title),  :
  Argument 'author_at_r' is missing, using default.
Warning in read.dcf(path) :
  cannot open compressed file '', probable reason 'No such file or directory'
Error in read.dcf(path) : cannot open the connection
Calls: <Anonymous> ... suggests_dep -> read_dcf -> colnames -> is.data.frame -> read.dcf
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/packagetrackr.Rcheck/00install.out’ for details.
Packages required but not available:
  'lme4', 'flexsurv', 'survminer', 'SurvRegCensCov', 'systemfit',
  'IPDFileCheck', 'car', 'lmtest', 'effects', 'relaimpo', 'tm',
  'tidyverse', 'haven'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/packHV.Rcheck/00install.out’ for details.
Packages required but not available: 'doParallel', 'FactoMineR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘penalized’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'genbankr', 'Biostrings', 'GenomicAlignments', 'GenomicRanges',
  'IRanges'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pafdR.Rcheck/00install.out’ for details.
Packages required but not available:
  'magicaxis', 'networkDynamic', 'mapproj'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/paf.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ggpubr’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pafr.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘devtools’
Package suggested but not available for checking: ‘WikidataR’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PAGI.Rcheck/00install.out’ for details.
Packages required but not available: 'irlba', 'N2R', 'R.utils', 'sccore'

Packages suggested but not available for checking:
  'AnnotationDbi', 'GO.db', 'org.Dr.eg.db', 'org.Hs.eg.db',
  'org.Mm.eg.db', 'pcaMethods', 'scde', 'uwot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'S4Vectors', 'Biostrings', 'vegan', 'GenomicRanges', 'plotly',
  'heatmaply', 'dendextend', 'ggfortify'

Packages suggested but not available for checking:
  'micropan', 'phangorn', 'pegas', 'DECIPHER', 'IRanges'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PAGWAS.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PairedData.Rcheck/00install.out’ for details.
pairsD3: no visible global function definition for ‘gray.colors’
Undefined global functions or variables:
  gray.colors
Consider adding
  importFrom("grDevices", "gray.colors")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘graph’

Packages suggested but not available for checking:
  'multcomp', 'alr4', 'scagnostics'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'MCPAN', 'coin', 'mcprofile'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rioja', 'vegan', 'ggrepel'

Packages suggested but not available for checking:
  'fields', 'gstat', 'tidyverse'

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

Packages which this enhances but not available for checking:
  'ashr', 'CorShrink', 'edgeR'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fitdistrplus’
Packages required but not available: 'GCD', 'raster', 'rgdal'

Packages suggested but not available for checking: 'agricolae', 'rworldmap'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘poems’

Package suggested but not available for checking: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'phangorn', 'phytools'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pals’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/palinsol.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘recipes’
Packages required but not available:
  'downloadthis', 'ggwordcloud', 'leaflet', 'plotly', 'RPostgreSQL'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/palm.Rcheck/00install.out’ for details.
Package required but not available: ‘partykit’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'raster', 'stars', 'viridis'
Running examples in ‘palr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: image_pal
> ### Title: Map data values to colours
> ### Aliases: image_pal image_raster image_stars
> 
> ### ** Examples
> 
> set.seed(28)
> vals <- sort(rnorm(100))
> cols <- image_pal(vals, zlim = c(-2.4, 2))
> plot(vals, col = cols); abline(h = 2)
> points(vals, pch  = 19, cex = 0.1) ## zlim excluded some of the range
> if (requireNamespace("raster", quietly = TRUE)) {
+ im <- image_raster(volcano)
+ library(raster)
+ plotRGB(im)
+ }
> if (!requireNamespace("stars", quietly = TRUE)) {
+ library(stars)
+ x <- st_as_stars(volcano)
+ plot(image_stars(x), rgb = 1:3)
+ }
Error in library(stars) : there is no package called ‘stars’
Execution halted
Package required but not available: ‘mapproj’

Package suggested but not available for checking: ‘latticeExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mc2d', 'PerMallows'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'heatmapFlex', 'R.utils', 'readmoRe', 'robustHD'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RSQLite', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lmerTest', 'lme4'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'PAMmisc', 'gam', 'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pampe.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pamr.Rcheck/00install.out’ for details.
Package required but not available: ‘coin’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'smoothmest', 'msm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'sylly.en', 'memisc', 'Epi', 'tseries', 'rms', 'forecast'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/panelaggregation.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Paneldata.formula: no visible global function definition for
  ‘model.frame’
Paneldata.formula: no visible global function definition for
  ‘model.matrix’
Paneldata.formula: no visible global function definition for
  ‘model.response’
summary.Paneldata: no visible global function definition for ‘coef’
summary.Paneldata: no visible global function definition for ‘pt’
Undefined global functions or variables:
  coef model.frame model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix",
             "model.response", "pt")
to your NAMESPACE file.
Package required but not available: ‘CBPS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'lmerTest'

Packages suggested but not available for checking:
  'brms', 'broom.mixed', 'car', 'plm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PanJen.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘lme4’
Package required but not available: ‘readr’

Packages suggested but not available for checking: 'celestial', 'magicaxis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyverse', 'Hmisc'

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

Package which this enhances but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dtw’
Running ‘testthat.R’ [50s/78s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > ## testthat.R
  > ##
  > ## Copyright (C)  2017  Alexander Eckert
  > ##
  > ## This file is part of parallelDist.
  > ##
  > ## parallelDist is free software: you can redistribute it and/or modify it
  > ## under the terms of the GNU General Public License as published by
  > ## the Free Software Foundation, either version 2 of the License, or
  > ## (at your option) any later version.
  > ##
  > ## parallelDist is distributed in the hope that it will be useful, but
  > ## WITHOUT ANY WARRANTY; without even the implied warranty of
  > ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
  > ## GNU General Public License for more details.
  > ##
  > ## You should have received a copy of the GNU General Public License
  > ## along with parallelDist. If not, see <http://www.gnu.org/licenses/>.
  > 
  > library(testthat)
  > library(parallelDist)
  > 
  > # workaround for error "cannot open file 'startup.Rs': No such file or directory"
  > Sys.setenv("R_TESTS" = "")
  > test_check("parallelDist")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 371 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (testMatrixDTWDistances.R:39:1): (code run outside of `test_that()`) ──
  <packageNotFoundError/error/condition>
  Error in `library(dtw)`: there is no package called 'dtw'
  Backtrace:
      ▆
   1. └─base::library(dtw) at testMatrixDTWDistances.R:39:0
  ── Error (testMatrixListDTWDistances.R:88:1): (code run outside of `test_that()`) ──
  <packageNotFoundError/error/condition>
  Error in `library(dtw)`: there is no package called 'dtw'
  Backtrace:
      ▆
   1. └─base::library(dtw) at testMatrixListDTWDistances.R:88:0
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 371 ]
  Error: Test failures
  Execution halted
Packages required but not available:
  'snowfall', 'raster', 'caret', 'geoR', 'gstat', 'quantregForest',
  'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mailR’
Running examples in ‘ParallelLogger-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addDefaultEmailLogger
> ### Title: Add the default e-mail logger
> ### Aliases: addDefaultEmailLogger
> 
> ### ** Examples
> 
> mailSettings <- list(
+   from = "someone@gmail.com",
+   to = c("someone_else@gmail.com"),
+   smtp = list(
+     host.name = "smtp.gmail.com",
+     port = 465,
+     user.name = "someone@gmail.com",
+     passwd = "super_secret!",
+     ssl = TRUE
+   ),
+   authenticate = TRUE,
+   send = TRUE
+ )
> 
> # Setting test to TRUE in this example so we don't really send an e-mail:
> addDefaultEmailLogger(mailSettings, "My R session", test = TRUE)
Error: ‘mailR’ must be installed for this functionality.
Execution halted
Package suggested but not available for checking: ‘BatchJobs’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/parallelMCMCcombine.Rcheck/00install.out’ for details.
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'pcalg', 'Rgraphviz'
Running examples in ‘ParallelPC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: IDA_parallel
> ### Title: Estimate Total Causal Effects using the IDA_parallel Algorithm
> ### Aliases: IDA_parallel
> 
> ### ** Examples
> 
> ##########################################
> ## Using IDA_parallel without mem.efficeient
> ##########################################
> library(bnlearn)
> library(pcalg)
Error in library(pcalg) : there is no package called ‘pcalg’
Execution halted
Packages suggested but not available for checking:
  'AER', 'afex', 'BayesFactor', 'betareg', 'biglm', 'blme', 'brms',
  'cAIC4', 'car', 'cgam', 'ClassDiscovery', 'cplm', 'drc', 'DRR',
  'EGAnet', 'factoextra', 'FactoMineR', 'fpc', 'gam', 'gamlss',
  'glmmTMB', 'ivreg', 'lavaSearch2', 'lfe', 'lme4', 'lmerTest',
  'lmtest', 'M3C', 'MCMCglmm', 'mediation', 'metaBMA', 'metafor',
  'mfx', 'multcomp', 'nFactors', 'panelr', 'pbkrtest', 'PCDimension',
  'plm', 'PMCMRplus', 'PROreg', 'projpred', 'quantreg', 'rstanarm',
  'sjstats', 'survey', 'truncreg', 'WRS2'
Packages required but not available: 'TIMP', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘GGally’
'LazyData' is specified without a 'data' directory
Running ‘run-all.R’ [15s/22s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  > library(BBmisc)
  
  Attaching package: 'BBmisc'
  
  The following object is masked from 'package:base':
  
      isFALSE
  
  > library(ParamHelpers)
  > 
  > test_check("ParamHelpers")
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 1041 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_renderOptPathPlot.R:19:3): renderOptPathPlot ────────────────────
  Error in `requirePackages(c("GGally", "ggplot2"), why = "renderOptPathPlot", 
      default.method = "load")`: For renderOptPathPlot please install the following packages: GGally
  Backtrace:
      ▆
   1. └─ParamHelpers::renderOptPathPlot(op0, iter = 0, alpha = FALSE) at test_renderOptPathPlot.R:19:2
   2.   └─BBmisc::requirePackages(...)
   3.     └─BBmisc::stopf(...)
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 1041 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'pedtools', 'pedprobr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'kinship2', 'maxLik'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/paran.Rcheck/00install.out’ for details.
Package required but not available: ‘ggpubr’

Package suggested but not available for checking: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'mboost', 'party', 'caret', 'glmnet', 'doParallel'

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

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package in Depends field not imported from: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.formula.make: no visible global function definition for ‘formula’
regress: no visible global function definition for ‘lm’
regress: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  formula lm model.matrix
Consider adding
  importFrom("stats", "formula", "lm", "model.matrix")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘introduction-to-parcoords-.Rmd’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ParDNAcopy.Rcheck/00install.out’ for details.
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'msm', 'sn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking: 'speedglm', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Package required but not available: ‘readr’

Packages suggested but not available for checking:
  'rgdal', 'devtools', 'leaflet'

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

Package suggested but not available for checking: ‘xts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fitdistrplus', 'flexsurv'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/parsec.Rcheck/00install.out’ for details.
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'C50', 'dials', 'earth', 'ggrepel'
Package unavailable to check Rd xrefs: ‘mixOmics’
Package required but not available: ‘ssym’

Packages suggested but not available for checking: 'SMNCensReg', 'AER'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘TH.data’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/partDSA.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/partialOR.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ggraph’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown

Attaching package: 'particles'

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

    filter, simulate


Attaching package: 'tidygraph'

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

    filter

Quitting from lines 102-107 (intro.Rmd) 
Error: processing vignette ‘intro.Rmd’ failed with diagnostics:
there is no package called 'ggraph'
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/partitionMap.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ggcorrplot’
Error(s) in re-building vignettes:
  ...
--- re-building ‘extending-partition.Rmd’ using rmarkdown
--- finished re-building ‘extending-partition.Rmd’

--- re-building ‘introduction-to-partition.Rmd’ using rmarkdown
Quitting from lines 79-80 (introduction-to-partition.Rmd) 
Error: processing vignette ‘introduction-to-partition.Rmd’ failed with diagnostics:
there is no package called 'ggcorrplot'
--- failed re-building ‘introduction-to-partition.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘regtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘furrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'pmml', 'strucchange', 'vcd', 'AER', 'TH.data', 'coin', 'psychotree',
  'party'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/partykit.Rcheck/00install.out’ for details.
Packages required but not available: 'strucchange', 'coin'

Packages suggested but not available for checking:
  'TH.data', 'vcd', 'ipred', 'varImp'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pasadr.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PASenseWear.Rcheck/00install.out’ for details.
Package required but not available: ‘glmnet’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'copBasic', 'GGally', 'plotly'

Packages suggested but not available for checking:
  'doParallel', 'tidyverse', 'faraway', 'rms', 'PResiduals',
  'truncdist'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PASWR2.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PASWR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/patchSynctex.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘readr’
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(patentr)
  > 
  > test_check("patentr")
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 24 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (4)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-acquire.R:5:3): empty parameters return empty result ────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'readr'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-acquire.R:5:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base withOneRestart(expr, restarts[[1L]])
   4.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 24 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pathdiagram.Rcheck/00install.out’ for details.
Packages required but not available:
  'AnnotationDbi', 'doParallel', 'org.Hs.eg.db', 'ggraph', 'fpc',
  'R.utils', 'KEGGREST', 'KEGGgraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘pathlibr.Rmd’
Package required but not available: ‘timeSeries’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pathmodelfit.Rcheck/00install.out’ for details.
Package required but not available: ‘MplusAutomation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BART', 'metR', 'twang'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'GenomicFeatures', 'glmnet', 'survminer', 'caret', 'clusterProfiler'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Checking should be performed on sources prepared by ‘R CMD build’.
Packages required but not available:
  'raster', 'rgdal', 'Morpho', 'imager', 'vegan', 'geomorph',
  'ClusterR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Packages required but not available:
  'jetset', 'magic', 'Mfuzz', 'SelectBoost', 'tnet', 'WGCNA'

Packages suggested but not available for checking:
  'Biobase', 'c060', 'elasticnet', 'glmnet', 'biomaRt', 'repmis',
  'R.rsp'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pauwels2014.Rcheck/00install.out’ for details.
Packages required but not available: 'future.apply', 'geometry', 'lightr'

Packages suggested but not available for checking:
  'alphashape3d', 'imager', 'mapproj'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘kinship2’
Package required but not available: ‘ibd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DDD', 'phytools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pbdSLAP.Rcheck/00install.out’ for details.
Package required but not available: ‘lme4’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggraph', 'imager'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pbixr.Rcheck/00install.out’ for details.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PBNPA.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'PerformanceAnalytics', 'latticeExtra', 'doParallel'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pbo.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PBSadmb.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘maptools’
Malformed Description field: should contain one or more complete sentences.
Package required but not available: ‘tseries’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bigutilsr', 'mmapcharr', 'rmio'

Packages suggested but not available for checking: 'plotly', 'vcfR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'graph', 'RBGL', 'ggm', 'vcd'

Package suggested but not available for checking: ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'exact2x2', 'MCMCpack'

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
Skipping vignette re-building
Packages suggested but not available for checking: 'optmatch', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Package suggested but not available for checking: ‘readr’
Packages required but not available: 'ClassDiscovery', 'changepoint'

Package suggested but not available for checking: ‘nFactors’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'freqdom', 'fda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spatstat.random’
Package required but not available: ‘rstan’

Package suggested but not available for checking: ‘qgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'pcalg', 'graph', 'Hmisc', 'lme4', 'sommer', 'ggm'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bigstatsr', 'Rfast', 'Rfast2'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'distory', 'geiger', 'mvSLOUCH', 'phangorn', 'TreeSim', 'yuima'

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

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

Package suggested but not available for checking: ‘mvSLOUCH’

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

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

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

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PCovR.Rcheck/00install.out’ for details.
Packages required but not available:
  'doParallel', 'prodlim', 'riskRegression', 'pec'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'SYNCSA', 'picante', 'phylobase', 'vegan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'changepoint', 'chipPCR', 'ecp', 'fda.usc', 'MBmca', 'qpcR',
  'segmented'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘multtest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pcSteiner.Rcheck/00install.out’ for details.
Packages required but not available: 'stplanr', 'readr'

Packages suggested but not available for checking:
  'leaflet', 'tmap', 'tidyverse'

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

Package suggested but not available for checking: ‘fUnitRoots’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘imager’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PDE.Rcheck/00install.out’ for details.
Package required but not available: ‘plm’

Packages suggested but not available for checking:
  'car', 'lmtest', 'msm', 'pglm', 'splm'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'PythonInR', 'RSQLite'
'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.
pdist: no visible global function definition for ‘dist’
pdist: no visible global function definition for ‘new’
Undefined global functions or variables:
  dist new
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dist")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package required but not available: ‘quantreg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PDM.Rcheck/00install.out’ for details.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dendextend', 'tseries'

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

Packages suggested but not available for checking:
  'adabag', 'C50', 'caret', 'Cubist', 'doParallel', 'earth', 'ipred',
  'mda', 'party', 'partykit'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘orthopolynom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plm', 'car', 'coefplot', 'lmtest', 'papeR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
band.chol.cv: no visible global function definition for ‘cov’
pdsoft.cv: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ddalpha’

Package suggested but not available for checking: ‘viridis’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'leaflet', 'leaflet.extras', 'gganimate', 'readr'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘pdxTrees-vignette.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 45-50 (pdxTrees-vignette.Rmd) 
Error: processing vignette ‘pdxTrees-vignette.Rmd’ failed with diagnostics:
there is no package called 'readr'
--- failed re-building ‘pdxTrees-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘qlcMatrix’

Packages suggested but not available for checking: 'pder', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘future.apply’
Packages required but not available:
  'prodlim', 'rms', 'riskRegression', 'lava', 'timereg'

Packages suggested but not available for checking:
  'party', 'cmprsk', 'Hmisc'

Packages which this enhances but not available for checking:
  'crrstep', 'randomForestSRC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’
Error(s) in re-building vignettes:
  ...
--- re-building ‘datasets.Rmd’ using rmarkdown
--- finished re-building ‘datasets.Rmd’

--- re-building ‘fss.Rmd’ using rmarkdown
Quitting from lines 431-436 (fss.Rmd) 
Error: processing vignette ‘fss.Rmd’ failed with diagnostics:
there is no package called 'car'
--- failed re-building ‘fss.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'pedtools', 'pedprobr', 'forrel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PedCNV.Rcheck/00install.out’ for details.
Packages required but not available: 'survey', 'kinship2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pedigree.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘psqn’

Packages suggested but not available for checking:
  'R.rsp', 'kinship2', 'TruncatedNormal'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'TTR', 'PerformanceAnalytics', 'readr', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'forrel', 'pedprobr', 'pedtools', 'ribd', 'verbalisr', 'dvir',
  'ibdsim2', 'paramlink2', 'pedbuildr', 'segregatr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘kinship2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'snpStats', 'adegenet'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pegas.Rcheck/00install.out’ for details.
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'sn'

Package suggested but not available for checking: ‘tidySEM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
PEMM_fun : find.lambda: no visible global function definition for
  ‘optimize’
PEMM_fun: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov optimize
Consider adding
  importFrom("stats", "cov", "optimize")
to your NAMESPACE file.
Packages required but not available: 'loa', 'latticeExtra'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘globaltest’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/penalized.Rcheck/00install.out’ for details.
Package required but not available: ‘tgp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘future.apply’
Packages required but not available:
  'doParallel', 'glmnet', 'survcomp', 'magic', 'lcmm'

Packages suggested but not available for checking: 'survminer', 'ptmixed'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fda', 'latticeExtra', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PenCoxFrail.Rcheck/00install.out’ for details.
Package required but not available: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fda', 'latticeExtra', 'doParallel'

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

Packages suggested but not available for checking: 'cartography', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/penPHcure.Rcheck/00install.out’ for details.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pense.Rcheck/00install.out’ for details.
Package required but not available: ‘penalized’

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

Package suggested but not available for checking: ‘penalized’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘PARMA21del1_ident’
Package required but not available: ‘multcomp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘phytools’

Packages suggested but not available for checking:
  'dendextend', 'vcfR', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ltm', 'mirt', 'fda', 'Hmisc', 'irtoys'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'graph', 'RBGL'

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

Packages suggested but not available for checking:
  'dygraphs', 'Hmisc', 'quantmod', 'gamlss', 'gamlss.dist', 'quantreg',
  'plotly', 'ggpubr', 'RPESE', 'R.rsp', 'RobStatTM'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'DMwR', 'quantmod'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'AER', 'afex', 'BayesFactor', 'betareg', 'bigutilsr', 'blavaan',
  'brms', 'car', 'cplm', 'forecast', 'gamm4', 'glmmTMB', 'ICS',
  'ICSOutlier', 'lme4', 'lmtest', 'metafor', 'mlogit', 'multimode',
  'rstanarm', 'survey'
Package required but not available: ‘seriation’

Packages suggested but not available for checking:
  'gclus', 'dendextend', 'dendextendRcpp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'rms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
permalgorithm: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PerMallows.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PERMANOVA.Rcheck/00install.out’ for details.
Package required but not available: ‘coin’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ipred', 'party'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/permPATH.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘coin’
Running ‘perm.coin.check.R’ [0s/1s]
  Running ‘precision.problem.R’ [0s/1s]
  Running ‘wilcoxon.kruskal.trend.R’ [0s/1s]
Running the tests in ‘tests/perm.coin.check.R’ failed.
Complete output:
  > ## check perm against coin (ver 1.0-8 or greater)
  > library(perm)
  > library(coin)
  Error in library(coin) : there is no package called 'coin'
  Execution halted
Running the tests in ‘tests/precision.problem.R’ failed.
Complete output:
  > ## This is a hard two sample precision problem.
  > ## What makes it hard is that the sum of the 
  > ## first 2 values of y are the same as the sum
  > ## of the second two, and to get the correct 
  > ## answer you need to get them exactly equal
  > ## You should get the same answer regardless of 
  > ## whether you multiply y by a constant
  > ## Here both coin 1.0-8 and perm 0.9.1 give the correct answer
  > ## (earlier versions of coin had problems with this example)
  > library(coin)
  Error in library(coin) : there is no package called 'coin'
  Execution halted
Running the tests in ‘tests/wilcoxon.kruskal.trend.R’ failed.
Complete output:
  > ## Test that perm gives the same answers in some special cases
  > library(perm)
  > library(coin)
  Error in library(coin) : there is no package called 'coin'
  Execution halted
Package required but not available: ‘dabestr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Package required but not available: ‘magic’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘vegan’
Packages suggested but not available for checking:
  'buildmer', 'car', 'doParallel', 'lme4', 'viridis'
Running examples in ‘permutes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clusterperm.glm
> ### Title: Cluster-based permutation tests for time series data, based on
> ###   generalized linear models or other 'buildmer' models. This is an
> ###   alias for 'clusterperm.lm' provided for discoverability.
> ### Aliases: clusterperm.glm
> 
> ### ** Examples
> 
> ## Don't show: 
> perms <- clusterperm.glm(Fz ~ Deviant * Session,data=MMN[MMN$Time > 200 & MMN$Time < 205,],series.var=~Time,nperm=2)
Loading required namespace: buildmer
Failed with error:  ‘there is no package called ‘buildmer’’
Error in pkgcheck("buildmer") : 
  Please install the following missing package: buildmer
Calls: clusterperm.glm -> clusterperm.lm -> pkgcheck
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘buildmer.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'viridis''
Quitting from lines 62-63 (buildmer.Rmd) 
Error: processing vignette ‘buildmer.Rmd’ failed with diagnostics:
Please install the following missing package: viridis
--- failed re-building ‘buildmer.Rmd’

--- re-building ‘permutes.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'viridis''
Quitting from lines 69-70 (permutes.Rmd) 
Error: processing vignette ‘permutes.Rmd’ failed with diagnostics:
Please install the following missing package: viridis
--- failed re-building ‘permutes.Rmd’

SUMMARY: processing the following files failed:
  ‘buildmer.Rmd’ ‘permutes.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'perry', 'quantreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘perryExamples’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/perry.Rcheck/00install.out’ for details.
Package required but not available: ‘Biobase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: ‘raster’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'plotly'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'doParallel', 'mapproj'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RSQLite’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/peruse.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'readr', 'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘DiagrammeR’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rjags', 'msm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caper', 'picante', 'quantreg', 'vegan', 'FD', 'phytools'

Package suggested but not available for checking: ‘lme4’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fda', 'expm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PGEE.Rcheck/00install.out’ for details.
Package required but not available: ‘spdep’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'maxLik', 'plm'

Packages suggested but not available for checking: 'lmtest', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘JGL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'KrigInv', 'randtoolbox'

Package suggested but not available for checking: ‘anMC’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'diagram', 'wordcloud'
Package suggested but not available for checking: ‘plm’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pgsc.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pgTools.Rcheck/00install.out’ for details.
Packages required but not available:
  'finalfit', 'Hmisc', 'VIM', 'plotly', 'rcompanion', 'readr', 'robust'

Package suggested but not available for checking: ‘devtools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gsDesign’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ph2bye.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘gsDesign’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'factoextra', 'bipartite', 'smerc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'Biostrings', 'seqinr'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phangorn.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'readr', 'tidyverse'
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pharmaRTF)
  
  Attaching package: 'pharmaRTF'
  
  The following object is masked from 'package:graphics':
  
      text
  
  > library(assertthat)
  > library(huxtable)
  
  Attaching package: 'huxtable'
  
  The following objects are masked from 'package:pharmaRTF':
  
      align, align<-, bold, bold<-, font, font<-, font_size, font_size<-,
      header_rows, header_rows<-, italic, italic<-, set_align, set_bold,
      set_font, set_font_size, set_header_rows, set_italic
  
  > 
  > test_check("pharmaRTF")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 169 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_helpers.r:3:1): (code run outside of `test_that()`) ─────────────
  <packageNotFoundError/error/condition>
  Error in `library(readr)`: there is no package called 'readr'
  Backtrace:
      ▆
   1. └─base::library(readr) at test_helpers.r:3:0
  ── Error (test_rtf-code-generators.r:3:1): (code run outside of `test_that()`) ──
  <packageNotFoundError/error/condition>
  Error in `library(readr)`: there is no package called 'readr'
  Backtrace:
      ▆
   1. └─base::library(readr) at test_rtf-code-generators.r:3:0
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 169 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘advanced_usage.Rmd’ using rmarkdown
Quitting from lines 13-20 (advanced_usage.Rmd) 
Error: processing vignette ‘advanced_usage.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘advanced_usage.Rmd’

--- re-building ‘huxtable_tips.Rmd’ using rmarkdown
Quitting from lines 13-20 (huxtable_tips.Rmd) 
Error: processing vignette ‘huxtable_tips.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘huxtable_tips.Rmd’

--- re-building ‘pharmaRTF.Rmd’ using rmarkdown
Quitting from lines 13-20 (pharmaRTF.Rmd) 
Error: processing vignette ‘pharmaRTF.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘pharmaRTF.Rmd’

--- re-building ‘tf_from_file.Rmd’ using rmarkdown
Quitting from lines 13-21 (tf_from_file.Rmd) 
Error: processing vignette ‘tf_from_file.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘tf_from_file.Rmd’

SUMMARY: processing the following files failed:
  ‘advanced_usage.Rmd’ ‘huxtable_tips.Rmd’ ‘pharmaRTF.Rmd’
  ‘tf_from_file.Rmd’

Error: Vignette re-building failed.
Execution halted
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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pharmr.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘rjags’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'zeitgebr', 'behavr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘expm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phateR.Rcheck/00install.out’ for details.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘test.pdf’
Packages required but not available: 'glmnet', 'RMySQL'

Package suggested but not available for checking: ‘randomForestSRC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'readr'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phenModel.Rcheck/00install.out’ for details.
Packages required but not available: 'gstat', 'pheno'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'changepoint', 'daymetr', 'MODISTools'

Packages suggested but not available for checking: 'leaflet', 'plotly'

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

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

Packages suggested but not available for checking: 'fields', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'rgdal', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'strucchange', 'doParallel', 'raster'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'R.utils', 'snpStats'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PHeval.Rcheck/00install.out’ for details.
Packages required but not available: 'glmnet', 'lme4', 'viridis'

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

Package suggested but not available for checking: ‘lme4’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'tidyverse', 'lingtypology'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘splancs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘1khz.wav’ ‘snd.wav’
Packages suggested but not available for checking:
  'ggspectra', 'photobiologyWavebands'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/photobiologyFilters.Rcheck/00install.out’ for details.
Package required but not available: ‘readr’

Packages suggested but not available for checking:
  'hyperSpec', 'pavo', 'ggspectra', 'photobiologyWavebands'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggspectra', 'photobiologyWavebands'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/photobiologyLamps.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'photobiologyWavebands', 'ggspectra'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/photobiologyLEDs.Rcheck/00install.out’ for details.
Package required but not available: ‘photobiologyWavebands’

Package suggested but not available for checking: ‘ggspectra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'photobiologyWavebands', 'ggspectra'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/photobiologySensors.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'photobiologyWavebands', 'ggspectra'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/photobiologySun.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/photobiologyWavebands.Rcheck/00install.out’ for details.
Package required but not available: ‘MCMCpack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phyclust.Rcheck/00install.out’ for details.
Package required but not available: ‘phylobase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'geometry', 'raster', 'gdistance'
Running examples in ‘phylin-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: extract.val
> ### Title: Extact pairwise values from a matrix in a specified order.
> ### Aliases: extract.val
> ### Keywords: variogram kriging
> 
> ### ** Examples
> 
> 
> data(vipers)
> data(d.gen)
> 
> # calculate midpoints
> mp <- midpoints(vipers[,1:2])
Error in midpoints(vipers[, 1:2]) : 
  Package 'geometry' is needed for Delaunay triangulation.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘phylin_tutorial.Snw’ using Sweave

Error: processing vignette ‘phylin_tutorial.Snw’ failed with diagnostics:
 chunk 31 (label = midpoints) 
Error in midpoints(vipers[, 1:2]) : 
  Package 'geometry' is needed for Delaunay triangulation.

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

--- re-building ‘resistance_tutorial.Snw’ using Sweave

Error: processing vignette ‘resistance_tutorial.Snw’ failed with diagnostics:
 chunk 7 (label = conductanceraster) 
Error in library(gdistance) : there is no package called ‘gdistance’

--- 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
Package required but not available: ‘RNeXML’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'capushe', 'glmnet', 'LINselect'

Packages suggested but not available for checking:
  'doParallel', 'phytools', 'TreeSim'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dendextend’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘phylogram-vignette.Rmd’ using rmarkdown

Attaching package: 'ape'

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

    as.phylo

Quitting from lines 223-243 (phylogram-vignette.Rmd) 
Error: processing vignette ‘phylogram-vignette.Rmd’ failed with diagnostics:
there is no package called 'dendextend'
--- failed re-building ‘phylogram-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘future.apply’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggm', 'ggraph', 'phylolm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'phangorn', 'betapart', 'raster', 'vegan', 'dismo', 'rgeos', 'rgdal'

Package suggested but not available for checking: ‘mapproj’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'phyloseq', 'ggnetwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'adephylo', 'phylobase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘vegan’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phylotools.Rcheck/00install.out’ for details.
Packages required but not available: 'NHPoisson', 'phylobase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'latticeExtra'

Packages suggested but not available for checking:
  'pez', 'picante', 'INLA', 'MCMCglmm', 'phylolm', 'DHARMa', 'rr2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PhysActBedRest.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'RSQLite', 'rms'
Running examples in ‘PhysicalActivity-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: deliveryPred
> ### Title: Wrapper Function for Accelerometry data Preprocessing, Feature
> ###   Extraction, and Delivery Prediction
> ### Aliases: deliveryPred
> 
> ### ** Examples
> 
> data(deliveryData)
> 
> predictions <- deliveryPred(df = deliveryData, model = "GLM")
Warning in deliveryPreprocess(df = df) :
  .id unspecified - dummy ID created
Error: deliveryPrediction requires the rms package, please install it.
Execution halted
Package suggested but not available for checking: ‘childsds’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Everest.Rmd’ using rmarkdown
--- finished re-building ‘Everest.Rmd’

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

--- re-building ‘NeonatalVentilation.Rmd’ using rmarkdown
Quitting from lines 21-31 (NeonatalVentilation.Rmd) 
Error: processing vignette ‘NeonatalVentilation.Rmd’ failed with diagnostics:
there is no package called 'childsds'
--- failed re-building ‘NeonatalVentilation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘phytools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'clusterGeneration', 'expm', 'phangorn'

Package suggested but not available for checking: ‘geiger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'insol', 'FME'

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

Packages suggested but not available for checking: 'brglm', 'quantreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/picasso.Rcheck/00install.out’ for details.
Package required but not available: ‘MCMCpack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'FrF2', 'DoE.base', 'FrF2.catlg128'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rayrender’
Packages required but not available:
  'car', 'DiagrammeR', 'lme4', 'multcomp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘readr’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(piggyback)
  > Sys.setenv(piggyback_cache_duration=0)
  > test_check("piggyback")
  [ FAIL 1 | WARN 0 | SKIP 21 | PASS 2 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (15)
  • Sys.getenv("CBOETTIG_TOKEN") == "" is TRUE (5)
  • empty test (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-errors.R:10:5): Attempt upload without authentication ───────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'readr'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-errors.R:10:4
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base withOneRestart(expr, restarts[[1L]])
   4.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 21 | PASS 2 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'bit64', 'DiagrammeR', 'nanotime'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plotly’

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
Package suggested but not available for checking: ‘tidyverse’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pinnacle.data.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'devtools', 'tidyverse'
Error(s) in re-building vignettes:
  ...
--- re-building ‘pinochet.Rmd’ using rmarkdown
Quitting from lines 52-58 (pinochet.Rmd) 
Error: processing vignette ‘pinochet.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘pinochet.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'doParallel', 'irlba'

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

Packages suggested but not available for checking:
  'AzureStor', 'Microsoft365R', 'R.utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tidyverse’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Quitting from lines 119-141 (Introduction.Rmd) 
Error: processing vignette ‘Introduction.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
Packages suggested but not available for checking:
  'devtools', 'doParallel', 'hdrcde'
Package required but not available: ‘XML2R’

Packages suggested but not available for checking: 'RSQLite', 'ggsubplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rstan', 'bayesmix', 'rjags'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'RPostgreSQL', 'topicmodels'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PivotalR.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘httptest’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(httptest)
  Error in library(httptest) : there is no package called 'httptest'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pivotaltrackR.Rmd’ using rmarkdown
Quitting from lines 12-15 (pivotaltrackR.Rmd) 
Error: processing vignette ‘pivotaltrackR.Rmd’ failed with diagnostics:
there is no package called 'httptest'
--- failed re-building ‘pivotaltrackR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggbeeswarm', 'ggrepel', 'irr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘pixar_film_ratings.Rmd’ using rmarkdown
Quitting from lines 27-33 (pixar_film_ratings.Rmd) 
Error: processing vignette ‘pixar_film_ratings.Rmd’ failed with diagnostics:
there is no package called 'irr'
--- failed re-building ‘pixar_film_ratings.Rmd’

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

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
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pkdata.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggnetwork’

Package suggested but not available for checking: ‘sna’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'Biobase'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pkgmaker.Rcheck/00install.out’ for details.
Package required but not available: ‘ComplexHeatmap’

Package suggested but not available for checking: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PKI.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PKLMtest.Rcheck/00install.out’ for details.
PKmod: no visible global function definition for ‘deriv’
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
Package required but not available: ‘randtoolbox’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PKreport.Rcheck/00install.out’ for details.
Packages required but not available: 'forestplot', 'rtf'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pks.Rcheck/00install.out’ for details.
Packages required but not available: 'readr', 'tigris'

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

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'CVXR', 'partykit', 'psychotree'

Packages suggested but not available for checking:
  'BayesMallows', 'BradleyTerry2', 'PLMIX', 'StatRank', 'hyper2',
  'prefmod'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plac.Rcheck/00install.out’ for details.
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Hmisc’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/planar.Rcheck/00install.out’ for details.
Package required but not available: ‘sdpt3r’

Package suggested but not available for checking: ‘freegroup’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'raster', 'RStoolbox'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plantecowrap.Rcheck/00install.out’ for details.
Package required but not available: ‘quantreg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'GenomicRanges', 'VariantAnnotation', 'S4Vectors', 'Rsamtools',
  'rtracklayer', 'SummarizedExperiment'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘viridis’
Packages required but not available:
  'Biostrings', 'seqinr', 'Seurat', 'useful'

Packages suggested but not available for checking:
  'AnnotationDbi', 'doParallel', 'fda.usc', 'ggalluvial', 'ggrepel',
  'harmony', 'IRanges', 'org.Hs.eg.db', 'org.Mm.eg.db', 'phytools',
  'readr', 'SummarizedExperiment', 'vegan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘rms’

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gWidgets2', 'gWidgets2tcltk'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plfm.Rcheck/00install.out’ for details.
Package required but not available: ‘tgp’

Package suggested but not available for checking: ‘splancs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'R.utils', 'ggforce', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plink.Rcheck/00install.out’ for details.
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.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘irtoys’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggmcmc', 'MCMCpack', 'prefmod', 'StatRank', 'PlackettLuce'

Package suggested but not available for checking: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lmtest', 'maxLik'

Packages suggested but not available for checking:
  'AER', 'car', 'pder', 'lfe'

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

Packages suggested but not available for checking: 'phyloseq', 'factoextra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PLordprob.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plot3Drgl.Rcheck/00install.out’ for details.
Package required but not available: ‘ggtern’

Package suggested but not available for checking: ‘mlogit’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PlotContour.Rcheck/00install.out’ for details.
Packages required but not available:
  'gganimate', 'raster', 'rgeos', 'viridis'

Packages suggested but not available for checking:
  'mapdata', 'maptools', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mapproj', 'plotly'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_GMM
> ### Title: Plots Mixture Components from Gaussian Mixture Models
> ### Aliases: plot_GMM
> 
> ### ** Examples
> 
> set.seed(235)
> mixmdl <- mixtools::normalmixEM(faithful$waiting, k = 2)
Error in loadNamespace(x) : there is no package called ‘mixtools’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("plotGMM")
  *Attention*: `plotGMM` is no longer actively developed. Instead, use the expanded package, `plotmm`. Thanks!
  > 
  > test_check("plotGMM")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_plot_GMM.R:6:3): plot_GMM catches input errors ──────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'mixtools'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test_plot_GMM.R:6:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base withOneRestart(expr, restarts[[1L]])
   4.       └─base doWithOneRestart(return(expr), restart)
  ── Error (test_plot_GMM.R:14:5): plot_GMM successfully plots ───────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'mixtools'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test_plot_GMM.R:14:4
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base withOneRestart(expr, restarts[[1L]])
   4.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plothelper.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'R.utils', 'depmixS4'
Error(s) in re-building vignettes:
  ...
--- re-building ‘compare_depmixS4.Rmd’ using knitr
Quitting from lines 37-62 (compare_depmixS4.Rmd) 
Error: processing vignette ‘compare_depmixS4.Rmd’ failed with diagnostics:
there is no package called 'depmixS4'
--- failed re-building ‘compare_depmixS4.Rmd’

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

SUMMARY: processing the following file failed:
  ‘compare_depmixS4.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'Hmisc', 'quantreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘plotly’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'GGally', 'devtools', 'dendextend', 'maptools', 'rgeos'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plotly.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘devtools’
Error(s) in re-building vignettes:
  ...
--- re-building ‘plot.matrix.Rmd’ using rmarkdown
Warning in fa.stats(r = r, f = f, phi = phi, n.obs = n.obs, np.obs = np.obs,  :
  The estimated weights for the factor scores are probably incorrect.  Try a different factor score estimation method.
Warning in fac(r = r, nfactors = nfactors, n.obs = n.obs, rotate = rotate,  :
  An ultra-Heywood case was detected.  Examine the results carefully
Warning in fa.stats(r = r, f = f, phi = phi, n.obs = n.obs, np.obs = np.obs,  :
  The estimated weights for the factor scores are probably incorrect.  Try a different factor score estimation method.
Warning in fac(r = r, nfactors = nfactors, n.obs = n.obs, rotate = rotate,  :
  An ultra-Heywood case was detected.  Examine the results carefully
Warning in fa.stats(r = r, f = f, phi = phi, n.obs = n.obs, np.obs = np.obs,  :
  The estimated weights for the factor scores are probably incorrect.  Try a different factor score estimation method.
Warning in fac(r = r, nfactors = nfactors, n.obs = n.obs, rotate = rotate,  :
  An ultra-Heywood case was detected.  Examine the results carefully
Warning in fa.stats(r = r, f = f, phi = phi, n.obs = n.obs, np.obs = np.obs,  :
  The estimated weights for the factor scores are probably incorrect.  Try a different factor score estimation method.
Warning in fac(r = r, nfactors = nfactors, n.obs = n.obs, rotate = rotate,  :
  An ultra-Heywood case was detected.  Examine the results carefully
Quitting from lines 274-281 (plot.matrix.Rmd) 
Error: processing vignette ‘plot.matrix.Rmd’ failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘plot.matrix.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mixtools', 'EMCluster', 'flexmix'
'LazyData' is specified without a 'data' directory
Running examples in ‘plotmm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_cut_point
> ### Title: Tidy Visualization of a Cut Point from a Mixture Model
> ### Aliases: plot_cut_point
> 
> ### ** Examples
> 
> if(require(mixtools)){
+ mixmdl <- mixtools::normalmixEM(faithful$waiting, k = 2)
+ }
Loading required package: mixtools
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘mixtools’
> plot_cut_point(mixmdl, plot = TRUE, color = "amerika") # returns plot, amerika
Error: Package "mixtools" needed for this function to work. Please install it.
Execution halted
Packages suggested but not available for checking:
  'C50', 'earth', 'glmnet', 'glmnetUtils', 'mlr', 'partykit', 'pre',
  'rpart.plot'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plotmo.Rcheck/00install.out’ for details.
Package required but not available: ‘seqinr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plotROC.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘MplusAutomation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘plotwidgets-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: modCol
> ### Title: Modify colors
> ### Aliases: contrastcol darkenCol modCol modhueCol saturateCol
> 
> ### ** Examples
> 
> plot.new()
> ## Loop over a few saturation / lightess values
> par(usr=c(-0.5, 0.5, -0.5, 0.5))
> v <- c(10, 9, 19, 9, 15, 5)
> pal <- plotPals("zeileis")
> for(sat in seq.int(-0.4, 0.4, length.out=5)) {
+   for(lgh in seq.int(-0.4, 0.4, length.out=5)) {
+     cols <- saturateCol(darkenCol(pal, by=sat), by=lgh)
+     wgPlanets(x=sat, y=lgh, w=0.16, h=0.16, v=v, col=cols)
+   }
+ }
Error in is.null(x) || is.na(x) : 
  'length = 24' in coercion to 'logical(1)'
Calls: wgPlanets -> .widgetWrapper -> .isnn
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plRasch.Rcheck/00install.out’ for details.
Package required but not available: ‘gamlss.dist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'FactoMineR', 'plspm'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plsdof.Rcheck/00install.out’ for details.
Package required but not available: ‘fields’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plsRglm', 'betareg'

Package suggested but not available for checking: ‘plsdof’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plsRglm', 'mixOmics', 'risksetROC', 'survcomp', 'survAUC', 'rms'

Package suggested but not available for checking: ‘plsdof’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bipartite', 'car'

Packages suggested but not available for checking:
  'plsdof', 'R.rsp', 'chemometrics'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package vignette with placeholder title ‘Vignette Title’:
  ‘introduction.Rmd’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/plsVarSel.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘readr’
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [60s/95s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(plumber)
  > 
  > test_check("plumber")
  [ FAIL 1 | WARN 0 | SKIP 18 | PASS 1893 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (13)
  • readr cannot be loaded (5)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-zzz-openapi.R:340:3): Response content type set with serializer ──
  Error in `serializer_csv()`: `readr` must be installed for `serializer_csv` to work
  Backtrace:
      ▆
   1. ├─plumber::pr_get(...) at test-zzz-openapi.R:340:2
   2. │ └─plumber::pr_handle(...)
   3. │   └─pr$handle(...)
   4. │     └─PlumberEndpoint$new(...)
   5. │       └─plumber initialize(...)
   6. └─plumber::serializer_csv()
  
  [ FAIL 1 | WARN 0 | SKIP 18 | PASS 1893 ]
  Error: Test failures
  Execution halted
checkRd: (7) ItemSelection-class.Rd:34-47: \item in \describe must have non-empty label
checkRd: (7) ItemSelection-class.Rd:59: \item in \describe must have non-empty label
checkRd: (7) ItemSelection-class.Rd:60: \item in \describe must have non-empty label
checkRd: (7) ItemSelection-class.Rd:61-62: \item in \describe must have non-empty label
checkRd: (7) ItemSelection-class.Rd:63-64: \item in \describe must have non-empty label
checkRd: (7) ItemSelection-class.Rd:65-67: \item in \describe must have non-empty label
checkRd: (7) RegionSelection-class.Rd:25-38: \item in \describe must have non-empty label
checkRd: (7) RegionSelection-class.Rd:48-55: \item in \describe must have non-empty label
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
Packages suggested but not available for checking:
  'doParallel', 'itertools'
Packages required but not available:
  'clusterProfiler', 'glmnet', 'org.Hs.eg.db', 'survminer'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘MixSim’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pmclust.Rcheck/00install.out’ for details.
Packages required but not available: 'Rmpfr', 'kSamples'

Packages suggested but not available for checking:
  'car', 'multcomp', 'NSM3'

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

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

Package suggested but not available for checking: ‘MSnbase’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ada', 'arules', 'caret', 'forecast', 'glmnet', 'rattle'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pmml.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘pmml’
Running examples in ‘pmmlTransformations-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DiscretizeXform
> ### Title: Discretizes a continuous variable to a discrete one as indicated
> ###   by interval mappings. This is in accordance to the PMML element:
> ###   *Discretize*
> ### Aliases: DiscretizeXform
> ### Keywords: manip
> 
> ### ** Examples
> 
> # Load the pmmlTransformations package
>     library(pmmlTransformations)
>     library(pmml)
Error in library(pmml) : there is no package called ‘pmml’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘FunctionXform.Rmd’ using rmarkdown
Quitting from lines 31-34 (FunctionXform.Rmd) 
Error: processing vignette ‘FunctionXform.Rmd’ failed with diagnostics:
there is no package called 'pmml'
--- failed re-building ‘FunctionXform.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘R.utils’

Packages suggested but not available for checking:
  'bigrquery', 'doParallel', 'RMariaDB', 'RPostgres', 'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Packages required but not available: 'condMVNorm', 'MCMCpack'

Package suggested but not available for checking: ‘rtdists’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DiagrammeR', 'ggrepel', 'gghalves'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'survey'

Packages suggested but not available for checking:
  'convey', 'lavaan.survey', 'srvyr', 'surf', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pnmtrem.Rcheck/00install.out’ for details.
Packages required but not available: 'readr', 'survey'

Packages suggested but not available for checking:
  'convey', 'lavaan.survey', 'srvyr', 'surf', 'tidyverse'

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
Package suggested but not available for checking: ‘httptest’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pocketapi)
  > 
  > test_check("pocketapi")
  Error in library(httptest) : there is no package called 'httptest'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pocketapi.Rmd’ using rmarkdown
Quitting from lines 19-23 (pocketapi.Rmd) 
Error: processing vignette ‘pocketapi.Rmd’ failed with diagnostics:
there is no package called 'httptest'
--- failed re-building ‘pocketapi.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘EbayesThresh’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pocrm.Rcheck/00install.out’ for details.
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'abc', 'doParallel', 'gdistance', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'PUlasso', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'survey'

Packages suggested but not available for checking:
  'convey', 'lavaan.survey', 'srvyr', 'surf', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘COUNT’
checkRd: (7) logitBvs.Rd:99: \item in \describe must have non-empty label
checkRd: (7) logitBvs.Rd:113: \item in \describe must have non-empty label
checkRd: (7) logitBvs.Rd:130: \item in \describe must have non-empty label
checkRd: (7) negbinBvs.Rd:92: \item in \describe must have non-empty label
checkRd: (7) negbinBvs.Rd:98: \item in \describe must have non-empty label
checkRd: (7) negbinBvs.Rd:116: \item in \describe must have non-empty label
checkRd: (7) pogitBvs.Rd:144: \item in \describe must have non-empty label
checkRd: (7) pogitBvs.Rd:169: \item in \describe must have non-empty label
checkRd: (7) pogitBvs.Rd:193: \item in \describe must have non-empty label
checkRd: (7) pogitBvs.Rd:211: \item in \describe must have non-empty label
checkRd: (7) poissonBvs.Rd:101: \item in \describe must have non-empty label
checkRd: (7) poissonBvs.Rd:118: \item in \describe must have non-empty label
checkRd: (7) poissonBvs.Rd:134: \item in \describe must have non-empty label
Package required but not available: ‘SmarterPoland’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'arrow', 'duckdb', 'ggforce', 'RSQLite', 'RMySQL', 'RPostgres',
  'readr', 'dittodb', 'odbc'
Running examples in ‘pointblank-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: db_tbl
> ### Title: Get a table from a database
> ### Aliases: db_tbl
> 
> ### ** Examples
> 
> # You can use an in-memory database
> # table and supply an in-memory table
> # to it too:
> small_table_duckdb <- 
+   db_tbl(
+     table = small_table,
+     dbname = ":memory:",
+     dbtype = "duckdb"
+   )
Error: Accessing a DuckDB table requires the duckdb package:
* It can be installed with `install.packages("duckdb")`.
Execution halted
Running ‘testthat.R’ [1s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pointblank)
  
  Attaching package: 'pointblank'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  > library(dittodb)
  Error in library(dittodb) : there is no package called 'dittodb'
  Execution halted
Packages required but not available: 'gmm', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/POINT.Rcheck/00install.out’ for details.
Packages required but not available: 'dplR', 'TripleR', 'DescTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PoisBinNonNor.Rcheck/00install.out’ for details.
Package required but not available: ‘GenOrd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PoisNonNor.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PoisNor.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/poissonMT.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/poissonreg.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘hexSticker’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/poLCA.Rcheck/00install.out’ for details.
Package required but not available: ‘vegan’

Package suggested but not available for checking: ‘devtools’

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

Package suggested but not available for checking: ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyverse', 'car', 'rstatix'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'weights', 'survey', 'car'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tm', 'textir', 'glmnet'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'brms', 'repmis'

Packages suggested but not available for checking:
  'rstan', 'pollimetrydata'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/polyapost.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'spatstat.geom', 'rgeos'
Error(s) in re-building vignettes:
  ...
--- re-building ‘polyCub.Rmd’ using rmarkdown
Quitting from lines 174-176 (polyCub.Rmd) 
Error: processing vignette ‘polyCub.Rmd’ failed with diagnostics:
there is no package called 'spatstat.geom'
--- failed re-building ‘polyCub.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘polyfreqs-mcmc.out’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'doParallel', 'MDSMap'

Packages suggested but not available for checking:
  'Hmisc', 'polyRAD', 'updog', 'mappoly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'itertools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
Quitting from lines 146-150 (overview.Rmd) 
Error: processing vignette ‘overview.Rmd’ failed with diagnostics:
there is no package called 'lme4'
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'doParallel', 'Hmisc'

Packages suggested but not available for checking: 'mappoly', 'polymapR'

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

Packages suggested but not available for checking:
  'Rsamtools', 'GenomeInfoDb', 'Biostrings', 'GenomicRanges',
  'VariantAnnotation', 'SummarizedExperiment', 'S4Vectors', 'IRanges',
  'GenomicFeatures', 'adegenet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘adegenet’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/polySegratioMM.Rcheck/00install.out’ for details.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/POMaSPU.Rcheck/00install.out’ for details.
Packages required but not available: 'caret', 'ipred'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pom.Rcheck/00install.out’ for details.
Packages required but not available: 'doParallel', 'DiagrammeR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dvmisc', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'RSQLite', 'RMySQL'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rstan', 'brms', 'lme4'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘R2jags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'expm', 'MCMCpack'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'Hmisc', 'GA', 'devtools'
Package required but not available: ‘Epi’

Packages suggested but not available for checking: 'relsurv', 'mstate'

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

Packages suggested but not available for checking:
  'WhopGenome', 'BlockFeST'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adegenet', 'calibrate', 'dismo', 'R.utils', 'pegas', 'genetics',
  'rgdal', 'gdistance', 'vegan', 'mmod', 'GGally', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/popKorn.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pop.lion.Rcheck/00install.out’ for details.
Packages required but not available: 'adegenet', 'vegan', 'pegas'

Package suggested but not available for checking: ‘RClone’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/popReconstruct.Rcheck/00install.out’ for details.
Package required but not available: ‘fields’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/population.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pop.wolf.Rcheck/00install.out’ for details.
Packages required but not available: 'forecast', 'timetk', 'xts'

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

Package suggested but not available for checking: ‘httptest’

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

Packages suggested but not available for checking:
  'car', 'fGarch', 'FitAR', 'gstat', 'tseries', 'vars'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xts', 'PerformanceAnalytics'

Packages suggested but not available for checking:
  'quantmod', 'fGarch', 'Rglpk', 'ROI.plugin.glpk'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'PerformanceAnalytics', 'quantmod', 'R.utils', 'xts'

Packages suggested but not available for checking:
  'CVXR', 'ggfortify', 'readtext', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PortfolioEffectHFT.Rcheck/00install.out’ for details.
Packages required but not available: 'xts', 'modopt.matlab'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BDportfolio_optim
> ### Title: Portfolio Optimization by Benders decomposition
> ### Aliases: BDportfolio_optim
> 
> ### ** Examples
> 
> 
> library (Rsymphony)  
> library(Rglpk) 
Error in library(Rglpk) : there is no package called ‘Rglpk’
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/portfolio.Rcheck/00install.out’ for details.
Packages required but not available: 'MCMCpack', 'tseries'

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

Packages suggested but not available for checking:
  'PortfolioAnalytics', 'PerformanceAnalytics'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘rstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘caret’
Packages required but not available:
  'refund', 'denseFLMM', 'xlsx', 'cosinor2', 'accelerometry', 'ActCR',
  'ActFrag', 'GGIR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rgdal', 'rgeos', 'RPostgreSQL'

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

Package suggested but not available for checking: ‘lme4’

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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘multtest’
Package required but not available: ‘doParallel’

Package suggested but not available for checking: ‘cartography’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'haplo.stats', 'BIGDAWG'

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

Packages suggested but not available for checking:
  'Rmpfr', 'lmtest', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'naniar'

Package suggested but not available for checking: ‘httptest’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plotly', 'ggpubr', 'FactoMineR', 'factoextra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/powerCompRisk.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/powerGWASinteraction.Rcheck/00install.out’ for details.
Packages required but not available: 'expm', 'glmnet', 'lme4', 'lmerTest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'bootnet', 'qgraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
‘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.
Packages required but not available: 'complexplus', 'expm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘crossdes’
Error(s) in re-building vignettes:
  ...
--- re-building ‘ABE.Rmd’ using rmarkdown
--- finished re-building ‘ABE.Rmd’

--- re-building ‘DP.Rmd’ using rmarkdown
Quitting from lines 115-122 (DP.Rmd) 
Error: processing vignette ‘DP.Rmd’ failed with diagnostics:
there is no package called 'crossdes'
--- failed re-building ‘DP.Rmd’

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PPCI.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'factoextra', 'vegclust'
Error(s) in re-building vignettes:
  ...
--- re-building ‘fcm.Rmd’ using rmarkdown
Quitting from lines 45-48 (fcm.Rmd) 
Error: processing vignette ‘fcm.Rmd’ failed with diagnostics:
there is no package called 'factoextra'
--- failed re-building ‘fcm.Rmd’

--- re-building ‘upfc.Rmd’ using rmarkdown
Quitting from lines 46-49 (upfc.Rmd) 
Error: processing vignette ‘upfc.Rmd’ failed with diagnostics:
there is no package called 'factoextra'
--- failed re-building ‘upfc.Rmd’

SUMMARY: processing the following files failed:
  ‘fcm.Rmd’ ‘upfc.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ppcor.Rcheck/00install.out’ for details.
Packages required but not available: 'leaflet', 'rgdal', 'tmap'

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

Packages suggested but not available for checking: 'GGally', 'PPtreeViz'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'genlasso', 'cvCovEst', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'censable', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatstat.core', 'spatstat.geom', 'spatstat'

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

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rfast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'furrr', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘partykit’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'spdep', 'spatialreg', 'maptools'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/prabclus.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘NlcOptim’
Running examples in ‘pracma-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fmincon
> ### Title: Minimize Nonlinear Constrained Multivariable Function.
> ### Aliases: fmincon
> ### Keywords: optimize
> 
> ### ** Examples
> 
> # Classical Rosenbrock function
> n <- 10; x0 <- rep(1/n, n)
> fn <- function(x) {n <- length(x)
+     x1 <- x[2:n]; x2 <- x[1:(n - 1)]
+     sum(100 * (x1 - x2^2)^2 + (1 - x2)^2)
+ }
> # Equality and inequality constraints
> heq1 <- function(x) sum(x)-1.0
> hin1 <- function(x) -1 * x
> hin2 <- function(x) x - 0.5
> ub <- rep(0.5, n)
> 
> # Apply constraint minimization
> res <- fmincon(x0, fn, hin = hin1, heq = heq1)
Error in fmincon(x0, fn, hin = hin1, heq = heq1) : 
  Package 'NlcOptim' missing -- install from CRAN.
Execution halted
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Packages suggested but not available for checking:
  'doBy', 'samplingbook', 'survey'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘lmtest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘PerfMeas’
Package required but not available: ‘irr’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'tidyverse'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘PRDA.Rmd’ using rmarkdown
--- finished re-building ‘PRDA.Rmd’

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

--- re-building ‘retrospective.Rmd’ using rmarkdown
Quitting from lines 21-24 (retrospective.Rmd) 
Error: processing vignette ‘retrospective.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘retrospective.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/precintcon.Rcheck/00install.out’ for details.
Packages required but not available:
  'hdf5r', 'raster', 'rgdal', 'R.utils', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggrepel’
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-precisely.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

Warning: Removed 6 row(s) containing missing values (geom_path).
Quitting from lines 199-217 (introduction-to-precisely.Rmd) 
Error: processing vignette ‘introduction-to-precisely.Rmd’ failed with diagnostics:
there is no package called 'ggrepel'
--- failed re-building ‘introduction-to-precisely.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘R.cache’

Package suggested but not available for checking: ‘styler’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘caret’
Packages required but not available: 'glmnet', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggiraphExtra', 'TH.data'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages which this enhances but not available for checking:
  'AER', 'betareg', 'biglm', 'brglm', 'caret', 'earth', 'ff', 'ffbase',
  'gam', 'glmnet', 'glmx', 'lme4', 'mclogit', 'mda', 'mlogit', 'MNP',
  'plm', 'quantreg', 'sampleSelection', 'speedglm', 'survey',
  'truncreg'
Unknown package ‘ffbase’ in Rd xrefs
Packages required but not available: 'fitdistrplus', 'Renext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Packages required but not available: 'lme4', 'pbkrtest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'traineR', 'rpart.plot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'Matching'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'party'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'caret', 'forecast', 'TSPred', 'tseries'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/prefmod.Rcheck/00install.out’ for details.
Packages required but not available: 'gamlss.dist', 'spdep', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PreProcess.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'earth', 'glmnet', 'partykit'

Packages suggested but not available for checking:
  'doParallel', 'glmertree', 'mboost', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'haven', 'justifier'
Running examples in ‘preregr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: source
> ### Title: Programmatically constructing justifier elements
> ### Aliases: source dcsn jstf asrt srce decide decision assert justify
> 
> ### ** Examples
> 
> ### Programmatically create a partial justification object
> exampleAssertion <-
+   preregr::assert(
+     "This is an assertion",
+     source = c(
+       preregr::source('This is a first source'),
+       preregr::source('This is a second source')));
Error in preregr::assert("This is an assertion", source = c(preregr::source("This is a first source"),  : 
  You can't justify without the `justifier` package.
ℹ You can install it with:

install.packages('justifier');
Execution halted
Package required but not available: ‘marelac’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Hmisc’
'LazyData' is specified without a 'data' directory
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
'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
Packages required but not available: 'car', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'maptools', 'raster', 'rosm', 'rgdal'
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
Package required but not available: ‘rjags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'maxLik', 'raster', 'splancs', 'lme4'

Packages suggested but not available for checking: 'geoR', 'R.rsp', 'INLA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rgdal', 'GenKern', 'fields', 'gstat', 'maptools'

Package suggested but not available for checking: ‘geoR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'future.apply', 'phangorn', 'vcfR'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reclin', 'caret', 'strex'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘softImpute’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'bipartite', 'diagram', 'DiagrammeR', 'vegan'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/primer.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/primerTree.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘devtools’
basisplot: no visible global function definition for ‘abline’
basisplot: no visible global function definition for ‘text’
basisplot: no visible global function definition for ‘par’
plot.prinsimp: no visible global function definition for ‘screeplot’
plot.simpart: no visible global function definition for ‘par’
position_text: no visible global function definition for ‘par’
position_text: no visible global function definition for ‘strwidth’
simpart.formula: no visible global function definition for ‘terms’
simpart.formula: no visible global function definition for
  ‘model.matrix’
varperc: no visible global function definition for ‘lines’
varperc: no visible global function definition for ‘text’
varsimp: no visible global function definition for ‘points’
varsimp: no visible global function definition for ‘text’
varsimp: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline lines model.matrix par points screeplot strwidth terms text
Consider adding
  importFrom("graphics", "abline", "lines", "par", "points", "strwidth",
             "text")
  importFrom("stats", "model.matrix", "screeplot", "terms")
to your NAMESPACE file.
Package suggested but not available for checking: ‘AER’
Packages required but not available: 'AnnotationDbi', 'org.Hs.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package vignette with placeholder title ‘Vignette Title’:
  ‘priorcd.Rmd’
Found the following files/directories:
  ‘network.html’ ‘network_files’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PriorGen.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'gurobi', 'raster', 'tmap', 'viridis', 'readr'
Package required but not available: ‘raster’

Packages suggested but not available for checking: 'rgeos', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'raster', 'rgeos', 'doParallel', 'fasterize', 'exactextractr'

Packages suggested but not available for checking:
  'RandomFields', 'maptools', 'gurobi', 'rcbc', 'cplexAPI',
  'prioritizrdata'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DiagrammeR', 'rio'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tm’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PRISMA.Rcheck/00install.out’ for details.
Package required but not available: ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xts', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lme4', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'DescTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rsample’
Error(s) in re-building vignettes:
  ...
--- re-building ‘equivocal-zones.Rmd’ using rmarkdown

Attaching package: 'probably'

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

    as.factor, as.ordered


Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

--- finished re-building ‘equivocal-zones.Rmd’

--- re-building ‘where-to-use.Rmd’ using rmarkdown
Quitting from lines 29-46 (where-to-use.Rmd) 
Error: processing vignette ‘where-to-use.Rmd’ failed with diagnostics:
there is no package called 'rsample'
--- failed re-building ‘where-to-use.Rmd’

SUMMARY: processing the following file failed:
  ‘where-to-use.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ProbBayes.Rcheck/00install.out’ for details.
Package required but not available: ‘Biostrings’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/probFDA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ProbitSpatial.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/probout.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘fable’
Error(s) in re-building vignettes:
  ...
--- re-building ‘ProbReco-with-fable.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


Attaching package: 'tidyr'

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

    extract


Attaching package: 'purrr'

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

    set_names

Quitting from lines 28-36 (ProbReco-with-fable.Rmd) 
Error: processing vignette ‘ProbReco-with-fable.Rmd’ failed with diagnostics:
there is no package called 'fable'
--- failed re-building ‘ProbReco-with-fable.Rmd’

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

SUMMARY: processing the following file failed:
  ‘ProbReco-with-fable.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ProbYX.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'processmapR', 'DiagrammeR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'DiagrammeR', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'diagram', 'ggrepel', 'rrtable', 'semTools', 'predict3d'

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'vegan', 'doParallel'
Running examples in ‘ProcMod-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: is_euclid
> ### Title: Test if the distance matrix is euclidean.
> ### Aliases: is_euclid
> 
> ### ** Examples
> 
> library(vegan)
Error in library(vegan) : there is no package called ‘vegan’
Execution halted
Packages suggested but not available for checking:
  'logcondens', 'doParallel'
Package required but not available: ‘gam’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'KrigInv', 'pGPx', 'quantreg'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: validate_profile
> ### Title: Definition of the profile data format
> ### Aliases: validate_profile dm_from_profile
> 
> ### ** Examples
> 
> rprof_file <- system.file("samples/rprof/1.out", package = "profile")
> ds <- read_rprof(rprof_file)
> validate_profile(ds)
> 
> bad_ds <- ds
> bad_ds$samples <- NULL
> try(validate_profile(bad_ds))
Error in validate_profile(bad_ds) : 
  identical(undotted(names(x)), c("meta", "sample_types", "samples",  .... is not TRUE
> 
> if (rlang::is_installed("dm")) {
+   dm <- dm_from_profile(ds)
+   print(dm)
+   dm::dm_draw(dm)
+ }
── Metadata ────────────────────────────────────────────────────────────────────
Tables: `samples`, `locations`, `functions`, `samples_locations`
Columns: 13
Primary keys: 3
Foreign keys: 3
Error:
! `dm_draw()` needs the 'DiagrammeR' package. Do you need `install.packages("DiagrammeR")` ?
Backtrace:
    ▆
 1. └─dm::dm_draw(dm)
 2.   └─dm:::bdm_render_graph(graph, top_level_fun = "dm_draw")
 3.     ├─dm:::check_suggested("DiagrammeR", use = TRUE, top_level_fun = top_level_fun)
 4.     │ ├─base::withVisible(eval(mc, parent.frame()))
 5.     │ └─base::eval(mc, parent.frame())
 6.     │   └─base::eval(mc, parent.frame())
 7.     └─dm `<fn>`(packages = "DiagrammeR", use = TRUE, top_level_fun = top_level_fun)
 8.       └─rlang::abort(message)
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/profileR.Rcheck/00install.out’ for details.
Packages required but not available: 'magicaxis', 'celestial'

Packages suggested but not available for checking: 'ProFound', 'sn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Package suggested but not available for checking: ‘gamlss.dist’
Running ‘testthat.R’ [524s/496s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(profoc)
  > 
  > test_check("profoc")
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 111 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • debug_mode is not TRUE (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-losses.R:3:1): (code run outside of `test_that()`) ──────────────
  <packageNotFoundError/error/condition>
  Error in `library(gamlss.dist)`: there is no package called 'gamlss.dist'
  Backtrace:
      ▆
   1. ├─base::suppressPackageStartupMessages(library(gamlss.dist)) at test-losses.R:3:0
   2. │ └─base::withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
   3. └─base::library(gamlss.dist)
  ── Error (test-oracle.R:2:1): (code run outside of `test_that()`) ──────────────
  <packageNotFoundError/error/condition>
  Error in `library(gamlss.dist)`: there is no package called 'gamlss.dist'
  Backtrace:
      ▆
   1. ├─base::suppressPackageStartupMessages(library(gamlss.dist)) at test-oracle.R:2:0
   2. │ └─base::withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
   3. └─base::library(gamlss.dist)
  
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 111 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'sqldf', 'RSQLite'

Packages suggested but not available for checking: 'R.rsp', 'BayesianTools'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'magicaxis', 'celestial'

Packages suggested but not available for checking:
  'ProFit', 'imager', 'Rfast', 'doSNOW'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'graph', 'Rgraphviz'
Running examples in ‘proftools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: filterProfileData
> ### Title: Filter Profile Data
> ### Aliases: filterProfileData
> ### Keywords: programming utilities
> 
> ### ** Examples
> 
> pd <- readProfileData(system.file("samples", "glmEx.out", package="proftools"))
> plotProfileCallGraph(pd)
Error in loadNamespace(x) : there is no package called ‘graph’
Calls: plotProfileCallGraph ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘proftools.Rnw’ using knitr
Quitting from lines 231-232 (proftools.Rnw) 
Error: processing vignette ‘proftools.Rnw’ failed with diagnostics:
there is no package called 'graph'
--- failed re-building ‘proftools.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/prognosticROC.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'doFuture', 'future.apply', 'furrr'
Packages required but not available: 'vegan', 'geometry', 'plotly'

Packages suggested but not available for checking:
  'spdep', 'fields', 'dendextend', 'uwot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘EpiEstim’
Running ‘testthat.R’ [3s/5s]
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
  [ FAIL 1 | WARN 0 | SKIP 19 | PASS 75 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (19)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-project.R:321:3): Test instantaneous_R = TRUE ───────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'EpiEstim'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-project.R:321:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base withOneRestart(expr, restarts[[1L]])
   4.       └─base doWithOneRestart(return(expr), restart)
  
  [ 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
Packages required but not available: 'plotly', 'GameTheory', 'kappalab'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'RMySQL', 'RSQLite', 'RJDBC', 'xlsx', 'RPostgreSQL'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ProjectTemplate.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lme4', 'gamm4'

Packages suggested but not available for checking:
  'rstanarm', 'brms', 'glmnet', 'doParallel', 'future.callr',
  'doFuture'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ggpubr', 'strucchange', 'lmtest', 'prophet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'tmvtnorm', 'ff'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PropClust.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/prop.comb.RR.Rcheck/00install.out’ for details.
Packages required but not available: 'dygraphs', 'rstan', 'xts'

Package suggested but not available for checking: ‘readr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ALDEx2', 'Biobase', 'plotly', 'SDMTools', 'vegan'
Running ‘testthat.R’ [12s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(propr)
  > 
  > test_check("propr")
  |------------(25%)----------(50%)----------(75%)----------|
  |------------(25%)----------(50%)----------(75%)----------|
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 187 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-ANOVA.R:6:1): (code run outside of `test_that()`) ───────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'vegan'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-ANOVA.R:6:0
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base withOneRestart(expr, restarts[[1L]])
   4.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 187 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘httptest’
Package suggested but not available for checking: ‘cin’
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mirt', 'plink'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/proteomicdesign.Rcheck/00install.out’ for details.
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
Packages required but not available:
  'readr', 'imputeTS', 'modeest', 'torch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/protoclass.Rcheck/00install.out’ for details.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘AmigaFFH’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ProTrackR.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'Biostrings', 'GOSemSim', 'doParallel', 'org.Hs.eg.db'
Packages required but not available: 'plotly', 'ggrepel', 'readr'

Packages suggested but not available for checking:
  'proDA', 'dendextend', 'heatmaply', 'furrr', 'seriation', 'drc',
  'STRINGdb'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rdtLite', 'rdt'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rdt', 'rdtLite'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rdt', 'rdtLite'
Package suggested but not available for checking: ‘cba’
Packages required but not available: 'readr', 'seqinr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'liteq', 'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'glmnet', 'bigsnpr', 'MCMCpack', 'bigsparser', 'lmtest', 'propagate',
  'bigparallelr', 'bigstatsr'

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

Package suggested but not available for checking: ‘geomorph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'PogromcyDanych', 'PBImisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PSAgraphics.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/psbcGroup.Rcheck/00install.out’ for details.
Packages required but not available: 'rjags', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'R.oo', 'R.utils', 'R.cache', 'aroma.light'

Packages suggested but not available for checking:
  'Hmisc', 'R.rsp', 'R.devices'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'MCMCpack', 'car', 'lmtest', 'vcd'
Running examples in ‘pscl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: UKHouseOfCommons
> ### Title: 1992 United Kingdom electoral returns
> ### Aliases: UKHouseOfCommons
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(UKHouseOfCommons)
> tmp <- UKHouseOfCommons[,c("v1","v2","v3")] 
> summary(apply(tmp,1,sum))
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.9999  1.0000  1.0000  1.0000  1.0000  1.0001 
> 
> col <- rep("black",dim(tmp)[1])
> col[UKHouseOfCommons$coninc==1] <- "blue"
> col[UKHouseOfCommons$labinc==1] <- "red"
> col[UKHouseOfCommons$libinc==1] <- "orange"
> 
> library(vcd)
Error in library(vcd) : there is no package called ‘vcd’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘countreg.Rnw’ using Sweave

Error: processing vignette ‘countreg.Rnw’ failed with diagnostics:
 chunk 1 (label = preliminaries) 
Error in library("lmtest") : there is no package called ‘lmtest’

--- failed re-building ‘countreg.Rnw’

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

Error: Vignette re-building failed.
Execution halted
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.
Packages required but not available: 'rgeos', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rio', 'xlsx'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pseudo.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'rms', 'rsample', 'mitml', 'lme4', 'miceadds', 'car'

Package suggested but not available for checking: ‘readr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'intamap', 'gstat', 'automap', 'doParallel', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'partykit', 'party'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'MCMCglmm', 'pedigree'

Package suggested but not available for checking: ‘AICcmodavg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fields', 'plm', 'spatialreg', 'spdep'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Package suggested but not available for checking: ‘doParallel’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘seasonal.Rmd’ using rmarkdown
Loading required package: nlme
This is mgcv 1.8-40. For overview type 'help("mgcv-package")'.

Attaching package: 'dplyr'

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

    collapse

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'kableExtra'

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

    group_rows

Partial vignette evaluation
Quitting from lines 22-38 (seasonal.Rmd) 
Error: processing vignette ‘seasonal.Rmd’ failed with diagnostics:
there is no package called 'doParallel'
--- failed re-building ‘seasonal.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Skipping vignette re-building
Packages suggested but not available for checking: 'R.rsp', 'alabama'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/psqn.Rcheck/00install.out’ for details.
Packages required but not available:
  'metap', 'car', 'DAMisc', 'multcomp', 'ggrepel'

Package suggested but not available for checking: ‘L1pack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Running examples in ‘psr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ICC_long
> ### Title: Intra-class Correlation Coefficient (ICC) for a set of athlete
> ###   measurements, with the data in long format
> ### Aliases: ICC_long
> 
> ### ** Examples
> 
> subject <- c(1, 1, 1, 2, 2, 2, 3, 3, 3)
> trial <- c(1, 2, 3, 1, 2, 3, 1, 2, 3)
> metric_1 <- c(250, 258, 252, 279, 270, 277, 218, 213, 218)
> metric_2 <- c(10, 7, 10, 14, 18, 17, 11, 7, 8)
> metric_3 <- c(1214, 1276, 1289, 1037, 1010, 1069, 1481, 1465, 1443)
> ICC_long(subject, trial, metric_1, metric_2, metric_3)
Error in loadNamespace(x) : there is no package called ‘lme4’
Calls: ICC_long ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘psr-explained.Rmd’ using rmarkdown
Quitting from lines 102-103 (psr-explained.Rmd) 
Error: processing vignette ‘psr-explained.Rmd’ failed with diagnostics:
there is no package called 'lme4'
--- failed re-building ‘psr-explained.Rmd’

SUMMARY: processing the following file failed:
  ‘psr-explained.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘rstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'epiR', 'longpower', 'plotly', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'np', 'chngpt'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GSVA', 'mpmi'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PsumtSim.Rcheck/00install.out’ for details.
Package required but not available: ‘SuperLearner’

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

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

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

Packages suggested but not available for checking: 'effects', 'lmtest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'qgraph', 'VCA', 'IsingSampler', 'GA'

Packages suggested but not available for checking:
  'semPlot', 'graphicalVAR', 'metaSEM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'likert', 'mirt', 'multcomp'
Package required but not available: ‘partykit’

Packages suggested but not available for checking:
  'stablelearner', 'strucchange'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'lme4', 'graph', 'Rgraphviz'
‘gs+qpdf’ made some significant size reductions:
     compacted ‘intro.pdf’ from 705Kb to 445Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files
Package required but not available: ‘ez’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'lmerTest'

Packages suggested but not available for checking:
  'ggrepel', 'nFactors', 'qqplotr', 'semPlot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ltm', 'irtoys'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GGally', 'ez'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: apply_graph_theme
> ### Title: Apply multiple DiagrammeR global graph attributes
> ### Aliases: apply_graph_theme
> 
> ### ** Examples
> 
> exampleSpec <-
+   system.file("inst",
+               "extdata",
+               "example_dct_spec_1.dct",
+               package="psyverse");
> parsedSpecs <- load_dct_specs(exampleSpec);
> dctGraph <- parsedSpecs$output$basic_graph;
> dctGraph <- apply_graph_theme(dctGraph,
+                               c("color", "#0000AA", "node"),
+                               c("fillcolor", "#00FFFF", "node"));
Error: This function applies graph themes to a `DiagrammeR` object. Therefore, obviously, that object must first exist, and you need the `DiagrammeR` package to create it and work with it. Please install it using:

  install.packages('DiagrammeR');
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > require(testthat);
  Loading required package: testthat
  > testthat::test_check("psyverse");
  Loading required package: psyverse
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 0 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • empty test (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-loading-dct-specs-from-files.R:16:3): a dct specification from a file with a single dct specification is loaded correctly ──
  Error in `res$output$completeness_graph$last_node`: $ operator is invalid for atomic vectors
  Backtrace:
      ▆
   1. └─testthat::expect_equal(...) at test-loading-dct-specs-from-files.R:16:2
   2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
   3.     └─rlang::eval_bare(expr, quo_get_env(quo))
  ── Error (test-loading-dct-specs-from-files.R:46:3): a directory with dct specifications is loaded correctly ──
  Error in `res$output$completeness_graph$last_node`: $ operator is invalid for atomic vectors
  Backtrace:
      ▆
   1. └─testthat::expect_equal(...) at test-loading-dct-specs-from-files.R:46:2
   2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
   3.     └─rlang::eval_bare(expr, quo_get_env(quo))
  
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 0 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PTAk.Rcheck/00install.out’ for details.
Package required but not available: ‘doParallel’

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

Package suggested but not available for checking: ‘GeneCycle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘geometry’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ptinpoly.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'DiagrammeR', 'readr'
Packages required but not available: 'lme4', 'tweeDEseq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Biostrings', 'muscle', 'seqinr'

Package suggested but not available for checking: ‘KEGGREST’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ProjectTemplate’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ptspotter.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘plotly’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘seqinr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘doRNG’
Package required but not available: ‘R.utils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fulltext’
Packages required but not available:
  'ggformula', 'gtsummary', 'car', 'Epi', 'epiR', 'Hmisc', 'lmtest',
  'sjPlot'

Packages suggested but not available for checking:
  'ggfortify', 'lme4', 'rms', 'rstatix', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'metafor', 'MetaUtility'

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

Package suggested but not available for checking: ‘metafor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'prodlim', 'lava', 'multcomp'

Packages suggested but not available for checking: 'riskRegression', 'rms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘bibliometrix’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'wordcloud', 'tm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'R.utils', 'RSQLite', 'readr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pullword.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'BigQuic', 'glmnet'
Error(s) in re-building vignettes:
  ...
--- re-building ‘other-criteria.Rmd’ using rmarkdown
Quitting from lines 33-60 (other-criteria.Rmd) 
Error: processing vignette ‘other-criteria.Rmd’ failed with diagnostics:
error in evaluating the argument ‘x’ in selecting a method for function ‘as.matrix’: there is no package called 'glmnet'
--- failed re-building ‘other-criteria.Rmd’

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

SUMMARY: processing the following file failed:
  ‘other-criteria.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'AnnotationDbi', 'SummarizedExperiment', 'Rsamtools', 'Biobase',
  'S4Vectors', 'GenomicFeatures', 'GenomicAlignments'

Package suggested but not available for checking: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fda', 'fda.usc', 'monoClust'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pumilioR.Rcheck/00install.out’ for details.
Packages required but not available: 'ggpubr', 'readr'

Package suggested but not available for checking: ‘furrr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nls2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fda', 'itsadug'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lme4’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘doSNOW’

Packages suggested but not available for checking: 'caret', 'glmnet'

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
'LazyData' is specified without a 'data' directory
Packages required but not available: 'sqldf', 'tidyverse', 'readr'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dcmle', 'dclone'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pvcurveanalysis.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pvldcurve.Rcheck/00install.out’ for details.
Package required but not available: ‘bit64’

Packages suggested but not available for checking: 'furrr', 'plotly'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'MazamaCoreUtils', 'MazamaSpatialUtils', 'dygraphs', 'ggmap',
  'leaflet', 'mapproj', 'maptools', 'openair', 'raster', 'rgdal',
  'readr', 'slippymath', 'xts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'ez', 'phia', 'afex', 'MBESS', 'semTools', 'quantreg',
  'lmtest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PwrGSD.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pxR.Rcheck/00install.out’ for details.
Packages required but not available: 'maptools', 'rgeos'

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
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Q7.Rcheck/00install.out’ for details.
Packages required but not available: 'ggcorrplot', 'PMCMRplus', 'haven'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘lme4’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Packages required but not available: 'ggforce', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/QCA.Rcheck/00install.out’ for details.
Package required but not available: ‘QCA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arules', 'arc'

Packages suggested but not available for checking: 'arulesCBA', 'rCBA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘EWAS_QC_graph_effectsize.png’ ‘EWAS_QC_graph_precision.png’
  ‘EWAS_QC_legend.txt’ ‘sample1.txt.gz’ ‘sample2.txt.gz’
  ‘sample_map.txt.gz’ ‘sample_output.graph_M.png’
  ‘sample_output.graph_QQ.png’ ‘sample_output.graph_p.png’
  ‘sample_output.graph_volcano.png’ ‘sample_output.histo.png’
  ‘sample_output.txt’ ‘sample_output1.graph_M.png’
  ‘sample_output1.graph_QQ.png’ ‘sample_output1.graph_p.png’
  ‘sample_output1.graph_volcano.png’ ‘sample_output1.histo.png’
  ‘sample_output2.graph_M.png’ ‘sample_output2.graph_QQ.png’
  ‘sample_output2.graph_p.png’ ‘sample_output2.graph_volcano.png’
  ‘sample_output2.histo.png’ ‘translation_table.txt’
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  ‘sample_QQ.png’ ‘sample_QQ1.png’ ‘sample_QQ2.png’ ‘sample_QQ3.png’
  ‘sample_distribution.png’ ‘sample_graph_p-correlation.png’
  ‘sample_histogram.png’ ‘sample_histogram1.png’
  ‘sample_histogram2.png’ ‘sample_histogram3.png’
  ‘sample_plots_graph_M.png’ ‘sample_plots_graph_QQ.png’
  ‘sample_precision.png’ ‘sample_regional_association.png’
  ‘sample_skewness_kurtosis.png’
Package required but not available: ‘ks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'quantreg', 'cSEM'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'tm', 'venneuler', 'wordcloud'

Package suggested but not available for checking: ‘koRpus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘qdapRegex-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: explain
> ### Title: Visualize Regular Expressions
> ### Aliases: explain
> ### Keywords: explain regex
> 
> ### ** Examples
> 
> explain("\\s*foo[A-Z]\\d{2,3}")
Warning in file(con, "r") :
  cannot open URL 'http://rick.measham.id.au/paste/explain.pl?regex=%5Cs*foo[A-Z]%5Cd%7B2,3%7D': HTTP status was '500 Internal Server Error'
Error in file(con, "r") : 
  cannot open the connection to 'http://rick.measham.id.au/paste/explain.pl?regex=%5Cs*foo[A-Z]%5Cd%7B2,3%7D'
Calls: explain -> readLines -> file
Execution halted
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("qdapRegex")
  > 
  > 
  > test_check("qdapRegex")
  [ FAIL 3 | WARN 2 | SKIP 0 | PASS 172 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-explain.R:5:5): explain produces a character vector ─────────────
  Error in `file(con, "r")`: cannot open the connection to 'http://rick.measham.id.au/paste/explain.pl?regex=(?%3C=foo)%5Cs%2B%5C(%5Cd%7B4%7D%5C)'
  Backtrace:
      ▆
   1. └─qdapRegex::explain("(?<=foo)\\s+\\(\\d{4}\\)") at test-explain.R:5:4
   2.   └─base::readLines(URL2)
   3.     └─base::file(con, "r")
  ── Error (test-rm_between.R:44:2): rm_between is extracting betweened text multiple markers ──
  Error in `left %in% c("'", "\"") && right %in% c("'", "\"")`: 'length = 2' in coercion to 'logical(1)'
  Backtrace:
      ▆
   1. ├─testthat::expect_equivalent(...) at test-rm_between.R:44:8
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─qdapRegex::rm_between(x, c("/", "@a"), c("#", "@b"), extract = TRUE)
  ── Error (test-rm_bracket.R:47:5): rm_bracket is extracting bracketed text ─────
  Error in `left %in% c("'", "\"") && right %in% c("'", "\"")`: 'length = 2' in coercion to 'logical(1)'
  Backtrace:
      ▆
   1. ├─testthat::expect_equivalent(...) at test-rm_bracket.R:47:4
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─qdapRegex::rm_bracket(...)
   5.   └─qdapRegex::rm_between(...)
  
  [ FAIL 3 | WARN 2 | SKIP 0 | PASS 172 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘pch’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'gamlss', 'gamlss.dist', 'vegan', 'Compositional'

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
Package required but not available: ‘R.utils’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'qgcomp', 'arm', 'future.apply'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arm', 'future.apply'

Package suggested but not available for checking: ‘devtools’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'FactoClass', 'FactoMineR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Hmisc', 'rms', 'cmprsk'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qlcMatrix.Rcheck/00install.out’ for details.
'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.
Package required but not available: ‘fitdistrplus’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qpcR.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/QPmin.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘distr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘qqconf_introduction.Rmd’ using rmarkdown
Loading required package: qqconf
Quitting from lines 204-213 (qqconf_introduction.Rmd) 
Error: processing vignette ‘qqconf_introduction.Rmd’ failed with diagnostics:
there is no package called 'distr'
--- failed re-building ‘qqconf_introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘calibrate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘lambda.pdf’ ‘qqplot.pdf’
Package suggested but not available for checking: ‘devtools’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qqplotr.Rcheck/00install.out’ for details.
Package required but not available: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'leaflet', 'raster'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'latticeExtra', 'lme4'

Packages suggested but not available for checking:
  'glmmTMB', 'gamlss', 'DHARMa'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'quantreg', 'truncSP'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lqr', 'quantreg'

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

Package suggested but not available for checking: ‘qrmtools’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'quantmod', 'Quandl', 'xts', 'rugarch'

Packages suggested but not available for checking: 'qrng', 'sn'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lqr', 'quantreg'

Package suggested but not available for checking: ‘qrLMM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘RSQLite’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'quantreg', 'msm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qtl2’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qtl2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'qtl2', 'ggrepel'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'qtl2', 'qtl2fst'

Package suggested but not available for checking: ‘qtl2ggplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'qtl2'
'LazyData' is specified without a 'data' directory
Running examples in ‘qtl2pleio-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convert_to_scan1_output
> ### Title: Convert 'scan_multi_oneqtl' output of 'qtl2::scan1' output
> ### Aliases: convert_to_scan1_output
> 
> ### ** Examples
> 
> # read data
> iron <- qtl2::read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
Error in loadNamespace(x) : there is no package called ‘qtl2’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [13s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(qtl2pleio)
  > 
  > test_check("qtl2pleio")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 76 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-boot_pvl.R:5:1): (code run outside of `test_that()`) ────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'qtl2'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-boot_pvl.R:5:0
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base withOneRestart(expr, restarts[[1L]])
   4.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 76 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bootstrap-cluster.Rmd’ using rmarkdown
Quitting from lines 181-182 (bootstrap-cluster.Rmd) 
Error: processing vignette ‘bootstrap-cluster.Rmd’ failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘bootstrap-cluster.Rmd’

SUMMARY: processing the following file failed:
  ‘bootstrap-cluster.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘RSQLite’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qtlc.Rcheck/00install.out’ for details.
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.
Packages required but not available:
  'glmnet', 'doParallel', 'QTL.gCIMapping'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qtlhot.Rcheck/00install.out’ for details.
Packages required but not available: 'sem', 'graph', 'pcalg'

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

Packages suggested but not available for checking: 'mappoly', 'devtools'

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

Packages suggested but not available for checking:
  'faraway', 'quantoptr', 'survminer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmx', 'np', 'quantreg'

Package suggested but not available for checking: ‘survey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'graph', 'RBGL'

Package suggested but not available for checking: ‘Rmpfr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'viridis', 'geometry'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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.
Packages suggested but not available for checking: 'elasticnet', 'glmnet'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/quadrupen.Rcheck/00install.out’ for details.
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/QualInt.Rcheck/00install.out’ for details.
Package required but not available: ‘leaflet’

Packages suggested but not available for checking: 'tigris', 'tidycensus'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘GGally’
Error(s) in re-building vignettes:
  ...
--- re-building ‘wilcox1973.Rmd’ using rmarkdown
Quitting from lines 111-120 (wilcox1973.Rmd) 
Error: processing vignette ‘wilcox1973.Rmd’ failed with diagnostics:
there is no package called 'GGally'
--- failed re-building ‘wilcox1973.Rmd’

SUMMARY: processing the following file failed:
  ‘wilcox1973.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/qualV.Rcheck/00install.out’ for details.
Packages required but not available: 'expm', 'Rfast', 'doParallel'

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

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

Package suggested but not available for checking: ‘timeSeries’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'np', 'quantreg', 'quantregGrowth'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'tm', 'lsa', 'quanteda.textmodels', 'quanteda.textplots', 'stm',
  'text2vec', 'topicmodels'
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart.Rmd’ using rmarkdown
Package version: 3.2.1
Unicode version: 14.0
ICU version: 71.1
Parallel computing: 4 of 32 threads used.
See https://quanteda.io for tutorials and examples.
Quitting from lines 323-328 (quickstart.Rmd) 
Error: processing vignette ‘quickstart.Rmd’ failed with diagnostics:
there is no package called 'quanteda.textplots'
--- failed re-building ‘quickstart.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘glmnet’

Packages suggested but not available for checking:
  'lsa', 'quanteda.textplots'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggrepel', 'sna'

Packages suggested but not available for checking:
  'quanteda.textmodels', 'wordcloud'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ExPosition’
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rstpm2’

Packages suggested but not available for checking:
  'fitdistrplus', 'lmtest', 'gk', 'OpVaR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'np', 'quantreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/quantities.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'xts', 'TTR'

Packages suggested but not available for checking:
  'RMySQL', 'RSQLite', 'timeSeries'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'GGally', 'sna'
Running examples in ‘QuantNorm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: connection.matrix
> ### Title: Construct connection matrix for network analysis
> ### Aliases: connection.matrix
> 
> ### ** Examples
> 
> 
> library(network); library(ggplot2); library(sna); library(GGally) #drawing network graph

‘network’ 1.17.1 (2021-06-12), part of the Statnet Project
* ‘news(package="network")’ for changes since last version
* ‘citation("network")’ for citation information
* ‘https://statnet.org’ for help, support, and other information

Error in library(sna) : there is no package called ‘sna’
Execution halted
Package required but not available: ‘quantreg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/quantregForest.Rcheck/00install.out’ for details.
Package required but not available: ‘quantreg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'quantreg', 'fda', 'Rearrangement'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/quantreg.Rcheck/00install.out’ for details.
Packages required but not available: 'quantreg', 'snowfall'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rugarch', 'smoots'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/quarrint.Rcheck/00install.out’ for details.
Package required but not available: ‘TreeTools’

Package suggested but not available for checking: ‘phangorn’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'styler', 'labelled'

Packages suggested but not available for checking: 'survey', 'Hmisc'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'rgeos', 'rgdal'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'rgdal', 'rgeos'

Package suggested but not available for checking: ‘fastshp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/quickpsy.Rcheck/00install.out’ for details.
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'spider', 'adegenet'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/quiddich.Rcheck/00install.out’ for details.
Packages required but not available: 'BayesFactor', 'MCMCpack'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘vroom’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'quantreg', 'ALDqr', 'MCMCpack'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'glmnet', 'flare'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fda’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/QZ.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/R0.Rcheck/00install.out’ for details.
Running examples in ‘R2019nCoV-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getDataFrame
> ### Title: Getting data.frame of detailed real-time statistical numbers of
> ###   every provinces of China of 2019-nCoV virus cases
> ### Aliases: getDataFrame
> 
> ### ** Examples
> 
> 
> x <- get_2019nCoV()
Error: parse error: premature EOF
                                       {"lastUpdateTime":"2022-04-30 1
                     (right here) ------^
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘R2019nCoV-introduction.Rmd’ using rmarkdown
Quitting from lines 34-35 (R2019nCoV-introduction.Rmd) 
Error: processing vignette ‘R2019nCoV-introduction.Rmd’ failed with diagnostics:
parse error: after key and value, inside map, I expect ',' or '}'
          ed":true,"tip":"","wzz_add":2}450900",!
                     (right here) ------^

--- failed re-building ‘R2019nCoV-introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘R2019nCoV-introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘ahaz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Error(s) in re-building vignettes:
  ...
--- re-building ‘R2admb.Rnw’ using knitr
Loading required package: stats4

Attaching package: 'bbmle'

The following object is masked from 'package:R2admb':

    stdEr

Warning: Removed 36 row(s) containing missing values (geom_path).
Warning: Removed 111 rows containing missing values (geom_point).
Quitting from lines 523-529 (R2admb.Rnw) 
Error: processing vignette ‘R2admb.Rnw’ failed with diagnostics:
there is no package called 'lme4'
--- failed re-building ‘R2admb.Rnw’

SUMMARY: processing the following file failed:
  ‘R2admb.Rnw’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'maptools', 'shapefiles', 'spdep', 'rgdal', 'spData', 'rgeos'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/R2BayesX.Rcheck/00install.out’ for details.
Package required but not available: ‘devtools’

Package suggested but not available for checking: ‘ReGenesees’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
conf2d.default: no visible global function definition for ‘polygon’
conf2d_int: no visible global function definition for ‘contourLines’
Undefined global functions or variables:
  contourLines polygon
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "polygon")
to your NAMESPACE file.
Package vignette with placeholder title ‘Vignette Title’:
  ‘R2DGC.Rmd’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggrepel’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lmerTest', 'pbkrtest', 'afex'

Package suggested but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘output.html’
Packages required but not available: 'rjags', 'R2WinBUGS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'broomExtra', 'rockchalk'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'R2WinBUGS', 'doParallel', 'memisc'

Packages suggested but not available for checking: 'doBy', 'car', 'lmtest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following calls to attach():
File ‘R2OpenBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
Packages suggested but not available for checking:
  'caret', 'earth', 'evtree', 'glmnet', 'mlr', 'partykit'
Package suggested but not available for checking: ‘devtools’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/r2sundials.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘RMark’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/R2WinBUGS.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/R330.Rcheck/00install.out’ for details.
Skipping vignette re-building
Packages suggested but not available for checking: 'R.rsp', 'BayesianTools'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/R4CouchDB.Rcheck/00install.out’ for details.
Package required but not available: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘r511-intro.Rmd’
Package required but not available: ‘raster’

Packages suggested but not available for checking: 'mapview', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'qgraph', 'sqldf'
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_R6causal.Rmd’ using rmarkdown
Quitting from lines 163-168 (using_R6causal.Rmd) 
Error: processing vignette ‘using_R6causal.Rmd’ failed with diagnostics:
Package "qgraph" needed for this plotting method to work. Please install it.
--- failed re-building ‘using_R6causal.Rmd’

SUMMARY: processing the following file failed:
  ‘using_R6causal.Rmd’

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
Package suggested but not available for checking: ‘RSQLite’
Package required but not available: ‘bayesmeta’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plotly', 'readr', 'dendextend', 'alakazam', 'tigger'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'asd', 'doParallel', 'multcomp', 'multxpert'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'FateID', 'fpc', 'irlba', 'vegan'

Packages suggested but not available for checking:
  'batchelor', 'DESeq2', 'SummarizedExperiment'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fasterize', 'raster', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'maptools', 'rgdal', 'rgeos', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'lme4', 'lmerTest', 'Hmisc', 'forestplot', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘radsafer’
Package required but not available: ‘caret’

Package suggested but not available for checking: ‘clValid’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'readr', 'plotly'

Packages suggested but not available for checking:
  'RSQLite', 'RPostgreSQL', 'odbc'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'radiant.data', 'radiant.basics', 'car', 'DiagrammeR', 'ggrepel',
  'pdp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'radiant.data', 'radiant.model', 'car', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'radiant.data', 'radiant.design', 'radiant.basics', 'radiant.model',
  'radiant.multivariate'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geometry', 'ptinpoly'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RAD.Rcheck/00install.out’ for details.
Package required but not available: ‘readr’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘cytofan’
Error(s) in re-building vignettes:
  ...
--- re-building ‘multivariate_analysis.Rmd’ using rmarkdown
Quitting from lines 15-31 (multivariate_analysis.Rmd) 
Error: processing vignette ‘multivariate_analysis.Rmd’ failed with diagnostics:
there is no package called 'cytofan'
--- failed re-building ‘multivariate_analysis.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'doParallel', 'glmnet', 'fastcmprsk'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'popdemo', 'DiagrammeR', 'Rcompadre'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'expm', 'Hmisc', 'snowfall', 'gRbase', 'RBGL', 'graph'

Package suggested but not available for checking: ‘KEGGgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rags2ridges', 'expm', 'Biobase', 'CGHbase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'R.cache', 'Quandl'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ragtop.Rcheck/00install.out’ for details.
Packages required but not available: 'hdrcde', 'ks'

Package suggested but not available for checking: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pegas', 'expm', 'Rfast', 'gaston'

Packages suggested but not available for checking:
  'plotly', 'haplotypes', 'adegenet', 'scatterpie', 'phylobase',
  'furrr', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'popdemo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dendextend', 'ggwordcloud'

Packages suggested but not available for checking:
  'tm', 'quanteda.textmodels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘readr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘readr’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘robotstxt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggrepel', 'imputeTS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ff', 'pcaMethods'

Packages suggested but not available for checking:
  'xcms', 'MSnbase', 'InterpretMSSpectrum'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘httptest’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RAMpath.Rcheck/00install.out’ for details.
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'tidyverse', 'plotly', 'RSQLite'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro-to-RaMS.Rmd’ using rmarkdown
Quitting from lines 105-107 (Intro-to-RaMS.Rmd) 
Error: processing vignette ‘Intro-to-RaMS.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘Intro-to-RaMS.Rmd’

--- re-building ‘RaMS-and-friends.Rmd’ using rmarkdown
Quitting from lines 86-109 (RaMS-and-friends.Rmd) 
Error: processing vignette ‘RaMS-and-friends.Rmd’ failed with diagnostics:
error in evaluating the argument ‘drv’ in selecting a method for function ‘dbConnect’: there is no package called 'RSQLite'
--- failed re-building ‘RaMS-and-friends.Rmd’

SUMMARY: processing the following files failed:
  ‘Intro-to-RaMS.Rmd’ ‘RaMS-and-friends.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘doParallel’

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
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'snowfall', 'orthopolynom', 'tmvtnorm', 'ks'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘raster’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RandomFields.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘RandomFields’
Packages required but not available: 'GGally', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (7) combine.Rd:31: invalid email address: andy\_liaw@merck.com
checkRd: (7) getTree.Rd:55: invalid email address: andy\_liaw@merck.com
checkRd: (7) grow.Rd:37: invalid email address: andy\_liaw@merck.com
checkRd: (7) partialPlot.Rd:79: invalid email address: andy\_liaw@merck.com
checkRd: (7) predict.randomForest.Rd:82: invalid email address: andy\_liaw@merck.com
checkRd: (7) predict.randomForest.Rd:83: invalid email address: matthew\_wiener@merck.com
checkRd: (7) randomForest.Rd:203: invalid email address: andy\_liaw@merck.com
checkRd: (7) randomForest.Rd:204: invalid email address: matthew\_wiener@merck.com
checkRd: (7) treesize.Rd:34: invalid email address: andy\_liaw@merck.com
checkRd: (7) varImpPlot.Rd:37: invalid email address: andy\_liaw@merck.com
Package required but not available: ‘BRISC’

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

Packages suggested but not available for checking:
  'pec', 'prodlim', 'caret', 'imbalance'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'Hmisc', 'geometry'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/randomizeR.Rcheck/00install.out’ for details.
Packages required but not available:
  'fastGHQuad', 'Rfast', 'doParallel', 'doRNG'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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

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

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/randtoolbox.Rcheck/00install.out’ for details.
Packages required but not available: 'distr', 'distrEx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'raster', 'rgdal', 'alphahull', 'rgeos', 'cleangeo'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'future.apply', 'RSQLite', 'raster', 'exactextractr'

Packages suggested but not available for checking: 'viridis', 'spdep'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'maptools', 'raster', 'rgdal', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'raster', 'rgdal', 'rgeos', 'spatstat', 'spocc', 'spThin'

Packages suggested but not available for checking:
  'BIEN', 'biomod2', 'dismo', 'ecospat', 'googlesheets'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘clValid’
Error(s) in re-building vignettes:
  ...
--- re-building ‘RankAggreg.Rnw’ using Sweave

Error: processing vignette ‘RankAggreg.Rnw’ failed with diagnostics:
 chunk 4 
Error in library(clValid) : there is no package called ‘clValid’

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

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘coin’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'coin', 'multcomp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rms’
Running examples in ‘rankhazard-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rankhazard-package
> ### Title: Rank-hazard plots
> ### Aliases: rankhazard-package rankhazard
> ### Keywords: package hplot survival
> 
> ### ** Examples
> 
> library(survival)
> model <- coxph(Surv(time,status) ~ age + sex + ph.karno, data = cancer, x=TRUE)
> rankhazardplot(model, data=cancer)
Y-axis range:  0.608 1.49 
 
Relative hazards for each covarite: 
          Min. 1st Qu. Median 3rd Qu. Max.
age      0.743   0.917      1    1.08 1.27
sex      0.608   0.608      1    1.00 1.00
ph.karno 0.766   0.875      1    1.07 1.49
> library(rms)
Error in library(rms) : there is no package called ‘rms’
Execution halted
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Errors in running code in vignettes:
when running code in ‘intro.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘intro.Rmd’ using ‘UTF-8’... failed to complete the test
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.
Packages required but not available:
  'graph', 'RBGL', 'NetPreProc', 'PerfMeas'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'devtools', 'readr', 'RJDBC', 'RMariaDB'

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
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'GenomicRanges', 'IRanges', 'bigsnpr', 'coloc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RapidPolygonLookup.Rcheck/00install.out’ for details.
Packages required but not available:
  'Biostrings', 'Rsamtools', 'GenomicRanges', 'GenomicAlignments'

Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RAppArmor.Rcheck/00install.out’ for details.
'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.
Package suggested but not available for checking: ‘tidyverse’
Error(s) in re-building vignettes:
  ...
--- re-building ‘modify.Rmd’ using rmarkdown
--- finished re-building ‘modify.Rmd’

--- re-building ‘sensitivity.Rmd’ using rmarkdown
Quitting from lines 18-20 (sensitivity.Rmd) 
Error: processing vignette ‘sensitivity.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘sensitivity.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'raster', 'adehabitatHR', 'RandomFields', 'doParallel', 'rgeos',
  'rgdal', 'hypervolume', 'ks'

Packages suggested but not available for checking: 'vegan', 'gurobi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'goodpractice'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'arules', 'sqldf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'adiv', 'geiger', 'vegan'

Packages suggested but not available for checking:
  'phyloregion', 'picante', 'phytools', 'raster'

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

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

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

Package suggested but not available for checking: ‘dendextend’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'car', 'RSNNS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'doParallel', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GGally', 'plotly', 'raster'

Package suggested but not available for checking: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘bcmaps’
Package required but not available: ‘raster’

Packages suggested but not available for checking:
  'doParallel', 'rasterVis', 'gstat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'fasterize'

Packages suggested but not available for checking: 'rasterVis', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rasterImage.Rcheck/00install.out’ for details.
Package required but not available: ‘raster’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'rgdal', 'rgeos', 'rasterVis', 'gstat', 'fields', 'exactextractr'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/raster.Rcheck/00install.out’ for details.
Packages required but not available: 'raster', 'latticeExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'geiger', 'phylolm', 'readr', 'mvMORPH'

Package suggested but not available for checking: ‘phytools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
rateratio.test: no visible global function definition for
  ‘complete.cases’
rateratio.test: no visible global function definition for ‘pbinom’
rateratio.test : p.L: no visible global function definition for ‘qbeta’
rateratio.test : p.U: no visible global function definition for ‘qbeta’
Undefined global functions or variables:
  complete.cases pbinom qbeta
Consider adding
  importFrom("stats", "complete.cases", "pbinom", "qbeta")
to your NAMESPACE file.
Package required but not available: ‘rstan’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'arrow', 'bit64', 'vroom'
Running examples in ‘RAthena-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RAthena_options
> ### Title: A method to configure RAthena backend options.
> ### Aliases: RAthena_options
> 
> ### ** Examples
> 
> library(RAthena)
> 
> # change file parser from default data.table to vroom
> RAthena_options("vroom")
Error: Please install vroom package and try again
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RatingScaleReduction.Rcheck/00install.out’ for details.
Package required but not available: ‘snowfall’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rationalfun.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘rpart.plot’

Packages suggested but not available for checking:
  'pmml', 'ada', 'arules', 'arulesViz', 'biclust', 'cairoDevice',
  'cba', 'doBy', 'fBasics', 'fpc', 'Hmisc', 'party', 'RGtk2', 'tm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gaston', 'mlogit', 'bedr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dipsaus', 'hdf5r', 'R.matlab', 'threeBrain'

Package suggested but not available for checking: ‘arrow’

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
Packages required but not available: 'DiagrammeR', 'dygraphs', 'xts'

Package suggested but not available for checking: ‘devtools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ChainLadder', 'devtools', 'fitdistrplus', 'readr'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘raster’
Package required but not available: ‘rayrender’

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

Package suggested but not available for checking: ‘spData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'raster'

Packages suggested but not available for checking:
  'viridis', 'rayrender', 'maptools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (7) coastlines.Rd:10: \item in \describe must have non-empty label
Package suggested but not available for checking: ‘raster’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rbacon.Rcheck/00install.out’ for details.
Package required but not available: ‘xts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'bit64', 'readr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rbent.Rcheck/00install.out’ for details.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘ggmap’

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

Package suggested but not available for checking: ‘rstanarm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'gam', 'RobStatTM'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Examples.Rmd’ using rmarkdown
Quitting from lines 206-219 (Examples.Rmd) 
Error: processing vignette ‘Examples.Rmd’ failed with diagnostics:
there is no package called 'gam'
--- failed re-building ‘Examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘raster’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'future.apply', 'nls2'

Package suggested but not available for checking: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rbi.helpers.Rcheck/00install.out’ for details.
Packages required but not available: 'rstan', 'ggmcmc', 'GGally'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rbiouml.Rcheck/00install.out’ for details.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Package required but not available: ‘mapproj’

Package suggested but not available for checking: ‘taxize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rbitcoinchartsapi.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘RBitmoji.Rmd’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘xts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'fts', 'xts'
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rblpapi.Rcheck/00install.out’ for details.
Packages required but not available: 'hdf5r', 'xts', 'dygraphs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rBMF.Rcheck/00install.out’ for details.
Packages required but not available: 'rstan', 'glmmTMB'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘latticeExtra’
Packages required but not available: 'earth', 'Hmisc'

Package suggested but not available for checking: ‘imbalance’

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

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
'LazyData' is specified without a 'data' directory
Package required but not available: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘survey’
Packages required but not available: 'R.oo', 'R.utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ff', 'ClustGeo', 'fields', 'raster', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'rgdal'

Packages suggested but not available for checking:
  'autothresholdr', 'conicfit'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RCAL.Rcheck/00install.out’ for details.
Package vignette with placeholder title ‘Vignette Title’:
  ‘rcane.Rmd’
Package required but not available: ‘rgdal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (7) closedp.Rd:150: \item in \describe must have non-empty label
checkRd: (7) closedp.Rd:151: \item in \describe must have non-empty label
checkRd: (7) closedp.Rd:152: \item in \describe must have non-empty label
checkRd: (7) closedp.Rd:153: \item in \describe must have non-empty label
checkRd: (7) closedp.Rd:154: \item in \describe must have non-empty label
Packages required but not available:
  'spatstat.geom', 'spatstat.core', 'spatstat.linnet', 'spatstat',
  'doSNOW'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RCA.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘spData’
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.
Package required but not available: ‘rgdal’

Packages suggested but not available for checking: 'rgeos', 'R.rsp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'optmatch', 'rrelaxiv'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rcbalance.Rcheck/00install.out’ for details.
Packages required but not available: 'arules', 'R.utils'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'REBayes', 'orthopolynom'

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

Packages suggested but not available for checking: 'rrelaxiv', 'optmatch'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.RData’
Packages required but not available: 'np', 'Benchmarking'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rcdklibs.Rcheck/00install.out’ for details.
Packages required but not available: 'rcdklibs', 'itertools'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘sqldf’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (7) Rcgmin.Rd:68-69: \item in \describe must have non-empty label
checkRd: (7) Rcgminb.Rd:56-57: \item in \describe must have non-empty label
checkRd: (7) Rcgminu.Rd:48-49: \item in \describe must have non-empty label
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'maptools', 'raster', 'readr', 'rgeos', 'dygraphs', 'xts', 'mapdata',
  'oceanmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rChoiceDialogs.Rcheck/00install.out’ for details.
Packages required but not available: 'maxLik', 'memisc', 'msm', 'plm'

Packages suggested but not available for checking:
  'car', 'lmtest', 'pglm', 'AER'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rworldmap’
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bit64’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘tm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'factoextra', 'FactoMineR', 'mda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
cmaOptimDP: no visible global function definition for ‘flush.console’
Undefined global functions or variables:
  flush.console
Consider adding
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Found the following files/directories:
  ‘outcmaesdisp.dat’
Packages required but not available: 'car', 'Hmisc', 'haven'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR', 'Rcmdr', 'viridis'

Package suggested but not available for checking: ‘rqubic’

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.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'crossdes', 'support.CEs', 'Rcmdr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcmdr', 'coin', 'multcomp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DCchoice', 'Rcmdr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'support.CEs', 'Rcmdr'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'DoE.base', 'FrF2', 'DoE.wrapper', 'Rcmdr', 'RcmdrMisc'

Package suggested but not available for checking: ‘FrF2.catlg128’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ez', 'Rcmdr', 'RcmdrMisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcmdr', 'epiR'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcmdr', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

Packages suggested but not available for checking:
  'car', 'cmprsk', 'meta', 'netmeta', 'multcomp', 'Matching',
  'survRM2', 'tableone', 'lmerTest', 'currentSurvival'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'FactoMineR', 'Rcmdr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GWRM', 'RcmdrMisc', 'Rcmdr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'HH', 'Rcmdr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

Packages suggested but not available for checking:
  'car', 'distr', 'distrEx', 'effects', 'lmtest', 'multcomp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lfstat', 'Rcmdr'

Package suggested but not available for checking: ‘lmomRFA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcmdr', 'metafor'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mixlm', 'phia', 'Rcmdr', 'car'

Packages suggested but not available for checking:
  'lme4', 'pbkrtest', 'vcd', 'multcomp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'orloca', 'orloca.es', 'Rcmdr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rrcov', 'Rcmdr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

Packages suggested but not available for checking:
  'qgraph', 'effects', 'vcd', 'car', 'gpairs', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcmdr', 'demography', 'forecast', 'ftsa'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcmdr', 'rjags'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'SCVA', 'Rcmdr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sos', 'Rcmdr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rcmdr', 'sutteForecastR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Rcmdr', 'Hmisc', 'tseries', 'lme4', 'distr', 'distrEx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tm', 'Rcmdr', 'latticeExtra'

Packages suggested but not available for checking:
  'ROpenOffice', 'tm.plugin.factiva', 'tm.plugin.lexisnexis',
  'tm.plugin.europresse', 'tm.plugin.alceste', 'twitteR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'IQCC', 'tseries', 'Rcmdr'

Package suggested but not available for checking: ‘car’

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.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RcmdrMisc', 'car', 'effects', 'lme4'

Packages suggested but not available for checking:
  'Hmisc', 'lmtest', 'multcomp', 'sem'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'R.utils', 'qgraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rcolombos.Rcheck/00install.out’ for details.
Package required but not available: ‘popdemo’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DescTools', 'coin', 'lmtest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘geoR’

Package suggested but not available for checking: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'haven', 'Hmisc', 'lmtest', 'survey', 'weights'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rcplex.Rcheck/00install.out’ for details.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RcppBigIntAlgos’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RcppBigIntAlgos.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'CensSpatial', 'StempCens'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Gauss: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Package suggested but not available for checking: ‘bit64’
'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.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘devtools’
Package suggested but not available for checking: ‘rredis’
Package suggested but not available for checking: ‘bit64’
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Package required but not available: ‘xts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'forecast', 'ggmap', 'leaflet', 'leafsync', 'pals', 'raster', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RCRnorm.Rcheck/00install.out’ for details.
Suggests orphaned package: ‘bibtex’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘lfe’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘tcpl’
Package suggested but not available for checking: ‘Mercator’
Packages suggested but not available for checking: 'raster', 'devtools'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RCzechia.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘devtools’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘vegan’

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
Package suggested but not available for checking: ‘ggpubr’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘Rdca.Rmd’ using rmarkdown
Quitting from lines 141-171 (Rdca.Rmd) 
Error: processing vignette ‘Rdca.Rmd’ failed with diagnostics:
there is no package called 'ggpubr'
--- failed re-building ‘Rdca.Rmd’

SUMMARY: processing the following file failed:
  ‘Rdca.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'AER', 'lmtest', 'R.utils'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lmtest', 'AER'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'AER', 'np', 'rdd', 'lmtest'

Package suggested but not available for checking: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'truncreg', 'maxLik'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (7) DecisionTree.Rd:464: \item in \describe must have non-empty label
checkRd: (7) DecisionTree.Rd:480: \item in \describe must have non-empty label
checkRd: (7) DecisionTree.Rd:495: \item in \describe must have non-empty label
'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.
Packages required but not available: 'R.oo', 'R.utils'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rgdal', 'haven'

Package suggested but not available for checking: ‘survey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bit64’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Packages required but not available: 'CVXR', 'maotai'

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
Package required but not available: ‘AER’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'chipPCR', 'qpcR', 'MBmca', 'shinyMolBio'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Biostrings', 'GOSemSim', 'doParallel', 'org.Hs.eg.db'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘cellWise’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'glmnet', 'devtools', 'R.utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rdroolsjars.Rcheck/00install.out’ for details.
'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’
Packages required but not available: 'Hmisc', 'ergm'

Package suggested but not available for checking: ‘survey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RDSTK.Rcheck/00install.out’ for details.
Package required but not available: ‘MCMCpack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘example.pdf’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rduino.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'leaflet', 'devtools', 'bit64', 'OSMscale', 'raster', 'R.utils',
  'readr', 'rgdal'
Packages required but not available: 'raster', 'rgrass7'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dataui’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/reactablefmtr.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘leaflet’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ReacTran.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'raster', 'rgdal', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/reader.Rcheck/00install.out’ for details.
Package required but not available: ‘R.utils’

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'haven', 'readr'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘R.utils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘vroom’

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
Package suggested but not available for checking: ‘MatrixExtra’
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readODS', 'streamR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘RSQLite’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RealVAMS.Rcheck/00install.out’ for details.
Package required but not available: ‘quantreg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plotly’
Running examples in ‘rearrr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: generate_clusters
> ### Title: Generate n-dimensional clusters
> ### Aliases: generate_clusters
> 
> ### ** Examples
> 
> # Attach packages
> library(rearrr)
> 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

> library(ggplot2)
> library(plotly)
Error in library(plotly) : there is no package called ‘plotly’
Execution halted
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/REBayes.Rcheck/00install.out’ for details.
'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: ‘devtools’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/recexcavAAR.Rcheck/00install.out’ for details.
'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.
Package required but not available: ‘ipred’

Packages suggested but not available for checking:
  'ddalpha', 'dials', 'rsample'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/reclin2.Rcheck/00install.out’ for details.
Package required but not available: ‘ldat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'vegan', 'picante', 'phangorn', 'phytools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘GA’

Package suggested but not available for checking: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘haven’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/recoder.Rcheck/00install.out’ for details.
Packages required but not available: 'imager', 'pavo', 'raster'

Package suggested but not available for checking: ‘smoothr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘MatrixExtra’

Package suggested but not available for checking: ‘recommenderlab’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘recommenderlab’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘recommenderlab’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arules', 'irlba'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘survminer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RSQLite', 'ff', 'ada', 'ipred'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘ggpubr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘RecordTest.Rmd’ using rmarkdown
Quitting from lines 11-31 (RecordTest.Rmd) 
Error: processing vignette ‘RecordTest.Rmd’ failed with diagnostics:
there is no package called 'ggpubr'
--- failed re-building ‘RecordTest.Rmd’

SUMMARY: processing the following file failed:
  ‘RecordTest.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'prevR', 'fields', 'move', 'rgeos'
Running examples in ‘recurse-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: drawCircle
> ### Title: Draws a circle
> ### Aliases: drawCircle
> 
> ### ** Examples
> 
> data(martin)
> revisits = getRecursions(martin, radius = 1)
> plot(revisits, martin, legendPos = c(10, -15))
Error: fields package needed for legend. Please install it.
Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(recurse)
  > 
  > test_check("recurse")
  [ FAIL 2 | WARN 1 | SKIP 1 | PASS 142 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • empty test (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_recurse.R:147:6): move objects ──────────────────────────────────
  Error in `move(x = df$x, y = df$y, time = df$t, proj = CRS("+proj=aeqd"), 
      animal = df$id)`: could not find function "move"
  Backtrace:
      ▆
   1. └─recurse createMoveObj(simplePts) at test_recurse.R:147:24
  ── Error (test_recurse.R:188:6): polygon ───────────────────────────────────────
  Error: rgeos package needed for this function to work. Please install it.
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test_recurse.R:188:19
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─recurse::getRecursionsInPolygon(track, poly)
   5. └─recurse:::getRecursionsInPolygon.data.frame(track, poly)
  
  [ FAIL 2 | WARN 1 | SKIP 1 | PASS 142 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘recurse.Rmd’ using rmarkdown
Loading required package: recurse
Loading required package: scales
Loading required package: sp
Quitting from lines 57-65 (recurse.Rmd) 
Error: processing vignette ‘recurse.Rmd’ failed with diagnostics:
fields package needed for legend. Please install it.
--- failed re-building ‘recurse.Rmd’

SUMMARY: processing the following file failed:
  ‘recurse.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Running examples in ‘REDCapExporter-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: build_r_data_package
> ### Title: Build R Data Package
> ### Aliases: build_r_data_package build_r_data_package.rcer_rccore
> ###   build_r_data_package.default
> 
> ### ** Examples
> 
> ## Please read the vignette for examples:
> ## vignette(topic = "export", package = "REDCapExporter")
> 
> library(REDCapExporter)
> # avs_raw_core <- export_core()
> data(avs_raw_core)
> tmppth <- tempdir()
> build_r_data_package(avs_raw_core, tmppth, author_roles = list(dewittp = c("cre", "aut")))
Warning in format_record.rcer_raw_record(x$record_raw, x$metadata_raw) :
  At least one of the columns is an S4 class.
  data.table might not work correctly for
  atoi, atoi_postseason
  check status of https://github.com/Rdatatable/data.table/issues/4315
  and https://github.com/dewittpe/REDCapExporter/issues/17
Creating source package at /home/hornik/tmp/scratch/Rtmp3aLkXx/rcd14465
Error in loadNamespace(x) : there is no package called ‘devtools’
Calls: build_r_data_package ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘api.Rmd’ using rmarkdown
--- finished re-building ‘api.Rmd’

--- re-building ‘export.Rmd’ using rmarkdown
Quitting from lines 72-76 (export.Rmd) 
Error: processing vignette ‘export.Rmd’ failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘export.Rmd’

SUMMARY: processing the following file failed:
  ‘export.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘odbc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'snowfall', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘REddyProc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘segmented’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ReDirection.Rcheck/00install.out’ for details.
Package required but not available: ‘speedglm’

Package suggested but not available for checking: ‘TCGAbiolinks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'readr'

Packages suggested but not available for checking:
  'leaflet', 'leafgl', 'rmapshaper', 'spdep'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'rgeos'

Packages suggested but not available for checking: 'devtools', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'BAT', 'dismo', 'gdistance', 'maptools', 'raster', 'rgdal', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘imager’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘AER’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/REEMtree.Rcheck/00install.out’ for details.
Package required but not available: ‘extremevalues’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘matchr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rgdal', 'spdep', 'MCMCglmm'

Package suggested but not available for checking: ‘maptools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘future.apply’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'VGAMdata', 'caret', 'expm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Suggests orphaned package: ‘bibtex’
Packages required but not available: 'ks', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'fda', 'magic', 'gamm4', 'lme4', 'RLRsim'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'plotly', 'refund'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bestglm', 'rpart.plot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘supercells’
Running ‘testthat.R’ [8s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(regional)
  > library(terra)
  terra 1.5.21
  
  Attaching package: 'terra'
  
  The following object is masked from 'package:testthat':
  
      describe
  
  > if (requireNamespace("sf", quietly = TRUE)) {
  +   library(sf)
  +   volcano = rast(system.file("raster/volcano.tif", package = "regional"))
  +   vr = read_sf(system.file("regions/volcano_regions.gpkg", package = "regional"))
  + 
  +   ortho = rast(system.file("raster/ortho.tif", package = "supercells"))
  +   vo = supercells::supercells(ortho, k = 1000, compactness = 1)
  + 
  +   test_check("regional")
  + }
  Linking to GEOS 3.10.2, GDAL 3.4.2, PROJ 9.0.0; sf_use_s2() is TRUE
  Error: [rast] filename is empty. Provide a valid filename
  Execution halted
Packages suggested but not available for checking: 'devtools', 'eurostat'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Regional_stats.Rmd’ using rmarkdown
Quitting from lines 18-20 (Regional_stats.Rmd) 
Error: processing vignette ‘Regional_stats.Rmd’ failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘Regional_stats.Rmd’

--- re-building ‘mapping.Rmd’ using rmarkdown
Quitting from lines 25-28 (mapping.Rmd) 
Error: processing vignette ‘mapping.Rmd’ failed with diagnostics:
there is no package called 'eurostat'
--- failed re-building ‘mapping.Rmd’

--- re-building ‘recode.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

--- finished re-building ‘recode.Rmd’

--- re-building ‘validation.Rmd’ using rmarkdown
--- finished re-building ‘validation.Rmd’

SUMMARY: processing the following files failed:
  ‘Regional_stats.Rmd’ ‘mapping.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘plgp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/reglogit.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'furrr', 'tidyverse', 'magic'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/regmed.Rcheck/00install.out’ for details.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'vioplot', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘broom.helpers’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'glmnet', 'rpart.plot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘usdm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘SSBtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'snowfall', 'GA', 'caret', 'glmnet', 'NlcOptim', 'semPlot'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/regsem.Rcheck/00install.out’ for details.
Package required but not available: ‘sjPlot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'R.utils', 'car', 'glmnet', 'text2vec'

Packages suggested but not available for checking: 'cdparcoord', 'partools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'CBPS', 'devtools'
Error(s) in re-building vignettes:
  ...
--- re-building ‘example-usage.Rmd’ using rmarkdown
Quitting from lines 59-75 (example-usage.Rmd) 
Error: processing vignette ‘example-usage.Rmd’ failed with diagnostics:
there is no package called 'CBPS'
--- failed re-building ‘example-usage.Rmd’

SUMMARY: processing the following file failed:
  ‘example-usage.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'qqman', 'R.utils', 'vcfR'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘doParallel’

Packages suggested but not available for checking: 'interval', 'Icens'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survey’

Package suggested but not available for checking: ‘care’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'Rgraphviz', 'Rglpk'

Packages which this enhances but not available for checking:
  'seriation', 'Rcplex'
Package unavailable to check Rd xrefs: ‘graph’
Running examples in ‘relations-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: choice
> ### Title: Relation-Based Choices
> ### Aliases: relation_choice
> ### Keywords: math
> 
> ### ** Examples
> 
> data("SVM_Benchmarking_Classification")
> ## Determine the three best classification learners in the above sense.
> relation_choice(SVM_Benchmarking_Classification, k = 3)
Error in loadNamespace(x) : there is no package called ‘Rglpk’
Calls: relation_choice ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘relations.Rnw’ using Sweave
Loading required package: Rgraphviz
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Rgraphviz’
Loading required package: Rgraphviz
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Rgraphviz’

Error: processing vignette ‘relations.Rnw’ failed with diagnostics:
 chunk 26 (label = consensus1b) 
Error in loadNamespace(x) : there is no package called ‘Rglpk’

--- failed re-building ‘relations.Rnw’

SUMMARY: processing the following file failed:
  ‘relations.Rnw’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/relaxo.Rcheck/00install.out’ for details.
Packages required but not available: 'Hmisc', 'densEstBayes'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggforce', 'xlsx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sna’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bde’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'relaimpo', 'Rmisc', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rcmdr’
Packages suggested but not available for checking: 'TTmoment', 'tmvtnorm'
Packages required but not available:
  'Familias', 'gWidgets2', 'gWidgets2tcltk'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘multicool’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pammtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RelValAnalysis.Rcheck/00install.out’ for details.
'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
Packages required but not available: 'JointAI', 'rjags', 'doFuture'

Package suggested but not available for checking: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘clusterGeneration’

Packages suggested but not available for checking: 'graph', 'Rgraphviz'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'latticeExtra', 'mapdata'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pbdRPC’
Package required but not available: ‘doParallel’

Package suggested but not available for checking: ‘statnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'AER', 'lme4', 'lmtest'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ismev’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Renext.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘devtools’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ReorderCluster.Rcheck/00install.out’ for details.
Package required but not available: ‘readr’

Packages suggested but not available for checking: 'RSQLite', 'RPostgres'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RepeatedHighDim.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/repeated.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/repello.Rcheck/00install.out’ for details.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lmerTest', 'pbkrtest'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatstat', 'spatstat.geom', 'spatstat.core'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘metafor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MBESS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'blavaan', 'rjags'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Repliscope.Rcheck/00install.out’ for details.
Package required but not available: ‘R.cache’

Package suggested but not available for checking: ‘xlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'lmerTest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'readr', 'survminer'
Packages suggested but not available for checking:
  'BayesFactor', 'brms', 'ivreg', 'lme4', 'rstanarm'
Error(s) in re-building vignettes:
  ...
--- re-building ‘cite_packages.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

--- finished re-building ‘cite_packages.Rmd’

--- re-building ‘new_models.Rmd’ using rmarkdown
--- finished re-building ‘new_models.Rmd’

--- re-building ‘report.Rmd’ using rmarkdown
Warning: Following variable(s) were not found: n_Obs
Warning: Following variable(s) were not found: n_Obs
Warning: Following variable(s) were not found: n_Obs
Warning in effectsize.htest(x, type = type, verbose = verbose, ...) :
  Unable to retrieve data from htest object. Using t_to_d() approximation.
Quitting from lines 131-136 (report.Rmd) 
Error: processing vignette ‘report.Rmd’ failed with diagnostics:
there is no package called 'lme4'
--- failed re-building ‘report.Rmd’

SUMMARY: processing the following file failed:
  ‘report.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/reporttools.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/REPPlab.Rcheck/00install.out’ for details.
Package required but not available: ‘REPPlab’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘styler’
Packages required but not available: 'metafor', 'lme4', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'RSQLite'

Packages suggested but not available for checking:
  'fasterize', 'gdalUtils', 'rgdal', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘leaflet’

Packages which this enhances but not available for checking:
  'plotly', 'geojsonio'
Packages required but not available: 'doParallel', 'flux'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/REQS.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/request.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘taxize’
Packages required but not available: 'plotdap', 'readr'

Packages suggested but not available for checking:
  'gganimate', 'mapdata', 'maptools', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/REREFACT.Rcheck/00install.out’ for details.
Package required but not available: ‘scam’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
.resampleMakeFunction: no visible global function definition for ‘is’
.resampleSetSeed: no visible global function definition for ‘runif’
CI.bca: no visible global function definition for ‘is’
CI.bca: no visible global function definition for ‘qnorm’
CI.bca: no visible global function definition for ‘pnorm’
CI.t: no visible global function definition for ‘qt’
ExpandProbs: no visible global function definition for ‘pnorm’
ExpandProbs: no visible global function definition for ‘qt’
colVars : f: no visible global function definition for ‘var’
colVars: no visible global function definition for ‘var’
hist.resample: no visible global function definition for ‘density’
hist.resample: no visible global function definition for ‘lines’
hist.resample: no visible global function definition for ‘points’
hist.resample: no visible global function definition for ‘approx’
hist.resample: no visible global function definition for ‘segments’
resample: no visible global function definition for ‘is’
samp.bootknife: no visible global function definition for ‘runif’
samp.bootstrap: no visible global function definition for ‘runif’
Undefined global functions or variables:
  approx density is lines pnorm points qnorm qt runif segments var
Consider adding
  importFrom("graphics", "lines", "points", "segments")
  importFrom("methods", "is")
  importFrom("stats", "approx", "density", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package required but not available: ‘irlba’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘doParallel’
Packages suggested but not available for checking:
  'haven', 'readr', 'RMariaDB', 'RPostgres', 'nodbi'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/resourcer.Rcheck/00install.out’ for details.
Packages required but not available: 'marelac', 'seacarb', 'segmented'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'marelac', 'segmented'

Packages suggested but not available for checking:
  'rMR', 'DiagrammeR', 'FishResp', 'respirometry'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘S4Vectors’

Package suggested but not available for checking: ‘rsolr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/restimizeapi.Rcheck/00install.out’ for details.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ic.infer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘useful’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RImageJROI', 'geometry', 'R.matlab'

Packages suggested but not available for checking:
  'gWidgets2RGtk2', 'gWidgets2', 'cairoDevice', 'RGtk2'

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
Packages required but not available: 'haven', 'labelled'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘furrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘evdbayes’
Unknown package ‘evdbayes’ in Rd xrefs
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/revealedPrefs.Rcheck/00install.out’ for details.
Packages required but not available: 'mipfp', 'truncdist'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/reverseR.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'bigrquery', 'redcapAPI', 'REDCapR', 'RPostgres', 'RSQLite'

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'RevGadgets'
Packages required but not available: 'plotly', 'tm', 'topicmodels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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.
Packages required but not available: 'rockchalk', 'lme4', 'plm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Hmisc’
Package suggested but not available for checking: ‘devtools’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rfacebook.Rcheck/00install.out’ for details.
Package required but not available: ‘Rfast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rfast.Rcheck/00install.out’ for details.
Package required but not available: ‘CCA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ConsensusClusterPlus', 'iCluster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rFDSN.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RfEmpImp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RFGLS.Rcheck/00install.out’ for details.
Package required but not available: ‘bit64’

Packages suggested but not available for checking: 'gganimate', 'R2jags'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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.
Packages required but not available: 'R.oo', 'R.utils', 'R.cache'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'readr', 'xts', 'TTR', 'PerformanceAnalytics'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'duckdb'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘FSA’
Running examples in ‘RFishBC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aStandard
> ### Title: Finds standard intercept (a) for Fraser-Lee back-calculation
> ###   model for a particular species.
> ### Aliases: aStandard
> ### Keywords: manip
> 
> ### ** Examples
> 
> aStandard("Bluegill")
Error in loadNamespace(x) : there is no package called ‘FSA’
Calls: aStandard ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘rworldmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rgdal’

Packages suggested but not available for checking: 'spdep', 'spData'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘MKomics’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RFLPtools.Rcheck/00install.out’ for details.
Packages required but not available: 'raster', 'rgdal'

Package suggested but not available for checking: ‘landscapemetrics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘raster’

Package suggested but not available for checking: ‘rgdal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GEOmap', 'splancs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘sos’
Packages required but not available: 'alphashape3d', 'geometry'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘swfscMisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'hdrcde', 'DiagrammeR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rfractran.Rcheck/00install.out’ for details.
.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
Packages required but not available: 'fda', 'plotly', 'Rssa'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'party', 'permimp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rfviz.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rga4gh.Rcheck/00install.out’ for details.
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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rGammaGamma.Rcheck/00install.out’ for details.
Packages required but not available: 'torch', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rgeos', 'raster'
Running ‘test-all.R’ [54s/77s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("rgbif")
  Loading required package: rgbif
  [ FAIL 2 | WARN 0 | SKIP 93 | PASS 931 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (93)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-wkt_large.R:68:3): wkt is used correctly in querying GBIF - occ_data ──
  Error: Please install rgeos
  Backtrace:
      ▆
   1. ├─vcr::use_cassette(...) at test-wkt_large.R:68:2
   2. │ └─cassette$call_block(...)
   3. ├─base::suppressMessages(...) at test-wkt_large.R:69:4
   4. │ └─base::withCallingHandlers(...)
   5. └─rgbif::occ_data(geometry = wkt, limit = 100, geom_big = "bbox")
   6.   └─rgbif .get_occ_data(curlopts = curlopts)
   7.     ├─tibble::as_tibble(prune_result(data))
   8.     └─rgbif:::prune_result(data)
   9.       └─rgbif:::check_for_a_pkg("rgeos")
  ── Error (test-wkt_large.R:83:3): wkt is used correctly in querying GBIF - occ_search ──
  Error: Please install rgeos
  Backtrace:
      ▆
   1. ├─vcr::use_cassette(...) at test-wkt_large.R:83:2
   2. │ └─cassette$call_block(...)
   3. ├─base::suppressMessages(...) at test-wkt_large.R:84:4
   4. │ └─base::withCallingHandlers(...)
   5. └─rgbif::occ_search(geometry = wkt, limit = 100, geom_big = "bbox")
   6.   └─rgbif .get_occ_search(curlopts = curlopts)
   7.     ├─tibble::as_tibble(...)
   8.     └─rgbif:::prune_result(setdfrbind(lapply(data, "[[", "data")))
   9.       └─rgbif:::check_for_a_pkg("rgeos")
  
  [ FAIL 2 | WARN 0 | SKIP 93 | PASS 931 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘sn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'RSQLite', 'maptools', 'mapview', 'rgeos'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rgdal.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rgdax.Rcheck/00install.out’ for details.
Packages required but not available: 'leaflet', 'leafem'

Packages suggested but not available for checking:
  'leaflet.extras2', 'geojsonio', 'stars', 'raster', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'RGENERATE', 'RMAWGEN'

Package suggested but not available for checking: ‘mapview’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RMAWGEN’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rgeoda.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RGeode.Rcheck/00install.out’ for details.
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'leaflet', 'pals', 'raster', 'spatstat.geom', 'splancs'

Packages suggested but not available for checking: 'leafsync', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'maptools', 'rgdal'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rgeos.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RGE.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘tmap’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Create_map_displaying_Ghana_2019_School_Attendance_Indicators.Rmd’ using rmarkdown
Quitting from lines 20-26 (Create_map_displaying_Ghana_2019_School_Attendance_Indicators.Rmd) 
Error: processing vignette ‘Create_map_displaying_Ghana_2019_School_Attendance_Indicators.Rmd’ failed with diagnostics:
there is no package called 'tmap'
--- failed re-building ‘Create_map_displaying_Ghana_2019_School_Attendance_Indicators.Rmd’

SUMMARY: processing the following file failed:
  ‘Create_map_displaying_Ghana_2019_School_Attendance_Indicators.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'raster', 'tmap', 'fields', 'mapview', 'stars'

Package suggested but not available for checking: ‘rgdal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rglpk.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'alphashape3d', 'webshot2'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RGoogleAnalyticsPremium.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RGoogleAnalytics.Rcheck/00install.out’ for details.
Package required but not available: ‘bit64’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'maptools', 'loa', 'leaflet'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ckanr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rgdal’

Package suggested but not available for checking: ‘chronosphere’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘grImport’

Packages suggested but not available for checking:
  'mapdata', 'party', 'quantmod', 'showtext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rgdal', 'RSQLite', 'stars'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rgrass7.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rgrass7’
Package required but not available: ‘RPostgres’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rGroovy.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rgr.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘stars’
Package required but not available: ‘RJDBC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RHawkes.Rcheck/00install.out’ for details.
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bit64’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘phytools’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
ggtree v3.4.0 For help: https://yulab-smu.top/treedata-book/

If you use the ggtree package suite in published research, please cite
the appropriate paper(s):

Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.
ggtree: an R package for visualization and annotation of phylogenetic
trees with their covariates and other associated data. Methods in
Ecology and Evolution. 2017, 8(1):28-36. doi:10.1111/2041-210X.12628

S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L
Zhan, T Wu, E Hu, Y Jiang, X Bo, G Yu. ggtreeExtra: Compact
visualization of richly annotated phylogenetic data. Molecular Biology
and Evolution. 2021, 38(9):4039-4042. doi: 10.1093/molbev/msab166

G Yu. Data Integration, Manipulation and Visualization of Phylogenetic
Trees (1st ed.). Chapman and Hall/CRC. 2022. ISBN: 9781032233574
Quitting from lines 40-46 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
there is no package called 'phytools'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘styler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Hmisc', 'GGally'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘mydata.rda’ ‘thedata.rda’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rHpcc.Rcheck/00install.out’ for details.
Packages required but not available: 'nonlinearTseries', 'lomb'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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
Packages required but not available: 'R.oo', 'R.utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'seqinr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ri2.Rcheck/00install.out’ for details.
Packages required but not available:
  'MCMCpack', 'msm', 'doParallel', 'BART', 'twang', 'RISCA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pedtools', 'kinship2'

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
Package required but not available: ‘vegan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readr’

Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo', 'forestmodel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RidgeFusion.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'CVXR', 'Rdimtools', 'T4cluster', 'maotai'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'forecast', 'xts'
Packages required but not available: 'xts', 'TTR', 'quantmod'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rifle.Rcheck/00install.out’ for details.
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.
Package suggested but not available for checking: ‘tidyverse’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'readr', 'haven'

Packages suggested but not available for checking: 'devtools', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'spatstat.geom', 'spatstat'

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
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘RInside/libs/RInside.so’:
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_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.
checkRd: (7) RInSp-package.Rd:44: invalid email address: dbprovete@gmail.com>
'LazyData' is specified without a 'data' directory
Package required but not available: ‘vegan’

Package suggested but not available for checking: ‘maptools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘haven’

Packages suggested but not available for checking:
  'bit64', 'arrow', 'readODS', 'readr'

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
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.
Packages required but not available:
  'relsurv', 'doParallel', 'glmnet', 'caret', 'SuperLearner'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rise.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘IsingSampler’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘mlogit’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘alabama’

Packages suggested but not available for checking:
  'portfolioBacktest', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cmprsk', 'doParallel', 'lava', 'mets', 'prodlim', 'Publish', 'rms',
  'timereg'

Packages suggested but not available for checking:
  'flexsurv', 'mstate', 'party', 'pec', 'penalized', 'randomForestSRC',
  'scam', 'SuperLearner', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/risksetROC.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/riskSimul.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Ritc.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘optmatch’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RItools.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘rgdal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘imputeTS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘maptools’
Error(s) in re-building vignettes:
  ...
--- re-building ‘riverplot-gallery.rmd’ using rmarkdown
Quitting from lines 78-104 (riverplot-gallery.rmd) 
Error: processing vignette ‘riverplot-gallery.rmd’ failed with diagnostics:
there is no package called 'maptools'
--- failed re-building ‘riverplot-gallery.rmd’

SUMMARY: processing the following file failed:
  ‘riverplot-gallery.rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rivivc.Rcheck/00install.out’ for details.
Packages required but not available: 'rrcov', 'quantreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rjags.Rcheck/00install.out’ for details.
Non-standard file/directory found at top level:
  ‘jri’
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 ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’

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 ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RJDBC.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ggdemetra’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘rjdmarkdown-html.Rmd’ using rmarkdown
Quitting from lines 47-59 (rjdmarkdown-html.Rmd) 
Error: processing vignette ‘rjdmarkdown-html.Rmd’ failed with diagnostics:
there is no package called 'ggdemetra'
--- failed re-building ‘rjdmarkdown-html.Rmd’

--- re-building ‘rjdmarkdown-pdf.Rmd’ using rmarkdown
Quitting from lines 53-65 (rjdmarkdown-pdf.Rmd) 
Error: processing vignette ‘rjdmarkdown-pdf.Rmd’ failed with diagnostics:
there is no package called 'ggdemetra'
--- failed re-building ‘rjdmarkdown-pdf.Rmd’

SUMMARY: processing the following files failed:
  ‘rjdmarkdown-html.Rmd’ ‘rjdmarkdown-pdf.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rjdqa.Rcheck/00install.out’ for details.
Package required but not available: ‘madness’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rJPSGCS.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘devtools’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RJSDMX.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rkafkajars.Rcheck/00install.out’ for details.
Package required but not available: ‘rkafkajars’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'pmml', 'arules'

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
Packages required but not available: 'maptools', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ComplexHeatmap', 'factoextra', 'FactoMineR', 'ggpubr'

Package suggested but not available for checking: ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'R.cache', 'highcharter', 'PTXQC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (7) hadr.Rd:29: \item in \value must have non-empty label
checkRd: (7) hulfun.Rd:29: \item in \value must have non-empty label
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rlabkey.Rcheck/00install.out’ for details.
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.
Package required but not available: ‘jrc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘doParallel’

Package suggested but not available for checking: ‘MCMCpack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rLFT.Rcheck/00install.out’ for details.
Packages required but not available: 'forecast', 'rstan', 'sn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'geometry', 'raster', 'rgeos', 'spatstat.geom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggrepel', 'irlba', 'doParallel', 'uwot', 'hdf5r'

Packages suggested but not available for checking:
  'Seurat', 'GenomicRanges', 'S4Vectors', 'IRanges', 'org.Hs.eg.db',
  'reactome.db', 'AnnotationDbi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rlinkedin.Rcheck/00install.out’ for details.
Package required but not available: ‘tseries’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'quantreg', 'magic'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘doParallel’

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
Package required but not available: ‘lme4’

Package which this enhances but not available for checking: ‘lmerTest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rLTP.Rcheck/00install.out’ for details.
Package required but not available: ‘doParallel’

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RLumModel.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [13s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > #! /usr/bin/env Rscript
  > 
  > library(testthat)
  > library(rly)
  > 
  > test_check("rly")
  Generating LALR tables 
  [ FAIL 1 | WARN 1 | SKIP 3 | PASS 190 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • empty test (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test.lex_literal4.R:20:3): literals as a string ──────────────────────
  Error in `!is.character(l) || nchar(l) > 1`: 'length = 3' in coercion to 'logical(1)'
  Backtrace:
       ▆
    1. ├─testthat::expect_output(rly::lex(Lexer), NA) at test.lex_literal4.R:20:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat .capture(...)
    4. │   │ └─testthat::capture_output_lines(code, print, width = width)
    5. │   │   └─testthat:::eval_with_output(code, print = print, width = width)
    6. │   │     ├─withr::with_output_sink(path, withVisible(code))
    7. │   │     │ └─base::force(code)
    8. │   │     └─base::withVisible(code)
    9. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   10. └─rly::lex(Lexer)
   11.   └─linfo$validate_all()
   12.     └─self$validate_literals()
  
  [ FAIL 1 | WARN 1 | SKIP 3 | PASS 190 ]
  Error: Test failures
  Execution halted
Found the following files/directories:
  ‘file.out’
Packages required but not available: 'GA', 'seriation'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘metafor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
ma.filter: no visible global function definition for ‘par’
ma.filter: no visible global function definition for ‘lines’
ma.filter: no visible global function definition for ‘abline’
qn: no visible global function definition for ‘lm’
qn: no visible global function definition for ‘var’
qn: no visible global function definition for ‘resid’
ss.filter: no visible global function definition for ‘smooth.spline’
ss.filter: no visible global function definition for ‘par’
ss.filter: no visible global function definition for ‘lines’
ss.filter: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline lines lm par resid smooth.spline var
Consider adding
  importFrom("graphics", "abline", "lines", "par")
  importFrom("stats", "lm", "resid", "smooth.spline", "var")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'Seurat', 'readr', 'viridis', 'phateR'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rmagic.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RMallow.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rmalschains.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'ggraph', 'mapview', 'taxize'
Packages required but not available: 'geojsonio', 'readr'

Packages suggested but not available for checking: 'rgdal', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geojsonio', 'rgdal', 'maptools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bit64’

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dygraphs’
Package required but not available: ‘msm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'R.oo', 'R.utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyverse’
Package required but not available: ‘vars’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ktaucenters’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rmcfs.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'lme4', 'merTools', 'AICcmodavg', 'pals'
Error(s) in re-building vignettes:
  ...
--- re-building ‘New_rmcorr_paper_analyses_figures.Rmd’ using rmarkdown
Quitting from lines 421-528 (New_rmcorr_paper_analyses_figures.Rmd) 
Error: processing vignette ‘New_rmcorr_paper_analyses_figures.Rmd’ failed with diagnostics:
could not find function "kelly"
--- failed re-building ‘New_rmcorr_paper_analyses_figures.Rmd’

SUMMARY: processing the following file failed:
  ‘New_rmcorr_paper_analyses_figures.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘questionr’
Running examples in ‘rmdformats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pilltabs
> ### Title: Given a cross-table, outputs HTML code to display several views
> ###   of with a tabbed interface
> ### Aliases: pilltabs
> 
> ### ** Examples
> 
> 
> data(airquality)
> tab <- table(airquality$Month, airquality$Ozone > 25)
> pilltabs(tab)
Error: the questionr package is needed for the pilltabs() function to work. Please install it.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rmdHelpers.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RMediation.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'rugarch', 'xts', 'Bessel', 'ff'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rMIDAS.Rcheck/00install.out’ for details.
Packages required but not available:
  'mda', 'adabag', 'party', 'Cubist', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rminizinc.Rcheck/00install.out’ for details.
Package required but not available: ‘ff’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tgp’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'latticeExtra', 'Hmisc'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rmisc.Rcheck/00install.out’ for details.
Package required but not available: ‘Rmixmod’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rmixmod.Rcheck/00install.out’ for details.
Package required but not available: ‘doParallel’

Packages suggested but not available for checking:
  'Rmixmod', 'blockcluster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'RMixtCompUtilities', 'RMixtCompIO', 'plotly'

Packages suggested but not available for checking:
  'Rmixmod', 'blockcluster', 'ClusVis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

Packages suggested but not available for checking:
  'RMixtCompIO', 'Rmixmod', 'blockcluster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
.pLGP_qvec: no visible global function definition for ‘ppois’
.qLGP_pvec: no visible global function definition for ‘qpois’
.rLGP.failsafe: no visible global function definition for ‘runif’
.subdmg: no visible global function definition for ‘dbinom’
dnegbin: no visible global function definition for ‘dnbinom’
pLGP: no visible global function definition for ‘ppois’
qLGP: no visible global function definition for ‘qpois’
rLGP: no visible global function definition for ‘rpois’
rLGP: no visible global function definition for ‘rnorm’
rLGP: no visible global function definition for ‘runif’
rbinegbin: no visible global function definition for ‘rnbinom’
rmanaclash: no visible global function definition for ‘rbinom’
rmanaclash: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbinom dnbinom ppois qpois rbinom rnbinom rnorm rpois runif
Consider adding
  importFrom("stats", "dbinom", "dnbinom", "ppois", "qpois", "rbinom",
             "rnbinom", "rnorm", "rpois", "runif")
to your NAMESPACE file.
Packages suggested but not available for checking: 'ff', 'recommenderlab'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RMOA.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘readr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘cheatsheet.Rmd’ using rmarkdown
--- finished re-building ‘cheatsheet.Rmd’

--- re-building ‘gff-processing.Rmd’ using rmarkdown
Quitting from lines 102-131 (gff-processing.Rmd) 
Error: processing vignette ‘gff-processing.Rmd’ failed with diagnostics:
there is no package called 'readr'
--- failed re-building ‘gff-processing.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
--- finished re-building ‘introduction.Rmd’

--- re-building ‘nozzle.Rmd’ using rmarkdown
--- finished re-building ‘nozzle.Rmd’

SUMMARY: processing the following file failed:
  ‘gff-processing.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ecr', 'cdata', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following calls to attach():
File ‘Rmosek/R/builder.R’:
  attach(builderenv, pos, name, warn.conflicts)
See section ‘Good practice’ in ‘?attach’.
Package suggested but not available for checking: ‘Bessel’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rmpfr.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rmpw.Rcheck/00install.out’ for details.
Package required but not available: ‘biglm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rms', 'rstan', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'readr', 'tbl2xts', 'PerformanceAnalytics', 'xts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
rms.pval: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages required but not available: 'Hmisc', 'quantreg', 'multcomp'

Packages suggested but not available for checking: 'plotly', 'rmsb'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Packages required but not available: 'pdp', 'strucchange', 'viridis'

Package suggested but not available for checking: ‘openair’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RMySQL.Rcheck/00install.out’ for details.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'AnnotationHub', 'AnnotationFilter', 'ensembldb', 'DESeq2',
  'SummarizedExperiment', 'vsn', 'ComplexHeatmap', 'ggrepel',
  'gghighlight'

Packages suggested but not available for checking: 'recount3', 'apeglm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RNAsmc.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘httptest’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("rnassqs")
  Loading required package: rnassqs
  Error in library(httptest) : there is no package called 'httptest'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Packages suggested but not available for checking:
  'rgdal', 'devtools', 'rnaturalearthhires', 'raster', 'rgeos'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RNaviCell.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘httptest’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rnbp)
  > 
  > test_check("rnbp")
  Error in library(httptest) : there is no package called 'httptest'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RNCBIEUtilsLibs.Rcheck/00install.out’ for details.
Packages required but not available: 'fields', 'tgp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gaston’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gaston’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rneos.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘bit64’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RNetLogo.Rcheck/00install.out’ for details.
Packages required but not available: 'tm', 'wordcloud'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rdflib', 'geiger', 'phytools', 'xslt'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RNeXML.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘survey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'gemtc', 'ggpubr', 'ggrepel', 'mcmcplots', 'netmeta', 'pcnetmeta',
  'R2jags'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Nnls.trimW : fun1: no visible global function definition for ‘runif’
initM: no visible global function definition for ‘runif’
rnmf: no visible global function definition for ‘txtProgressBar’
rnmf: no visible global function definition for ‘setTxtProgressBar’
see: no visible global function definition for ‘heat.colors’
see: no visible global function definition for ‘colorRampPalette’
see: no visible global function definition for ‘grey’
see: no visible global function definition for ‘par’
see: no visible global function definition for ‘image’
see: no visible global function definition for ‘mtext’
simtum: no visible global function definition for ‘runif’
simtum: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  colorRampPalette grey heat.colors image mtext par rnorm runif
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey", "heat.colors")
  importFrom("graphics", "image", "mtext", "par")
  importFrom("stats", "rnorm", "runif")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Packages required but not available: 'doParallel', 'speaq', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'taxize', 'raster', 'leaflet', 'rgdal', 'ggmap'
Packages required but not available: 'fields', 'GEOmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'raster', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rgdal', 'ggmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘arrow’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rrcov', 'distr', 'distrEx', 'distrMod', 'RandVar'

Package suggested but not available for checking: ‘ROptEst’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘pammtools’

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'cvTools', 'fda', 'rrcov', 'fpc', 'GGally', 'ggfortify',
  'robustHD', 'VIM', 'zCompositions'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
‘library’ or ‘require’ calls in package code:
  ‘robustbase’ ‘sfsmisc’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.BuildPartial: no visible global function definition for ‘as.formula’
.BuildPartial: no visible global function definition for ‘residuals’
.PairwiseCorrelation : .Standardize : <anonymous>: no visible global
  function definition for ‘na.omit’
.PairwiseCorrelation : .Standardize: no visible binding for global
  variable ‘median’
.PairwiseCorrelation: no visible global function definition for
  ‘complete.cases’
.yw: no visible global function definition for ‘toeplitz’
FastQn: no visible global function definition for ‘median’
FastQn: no visible global function definition for ‘mad’
fqn: no visible global function definition for ‘median’
fqn: no visible global function definition for ‘mad’
psdcor: no visible global function definition for ‘posdefify’
psdcor: no visible global function definition for ‘nearcor’
robar: no visible global function definition for ‘frequency’
robcor: no visible global function definition for ‘covMcd’
s_FastQn: no visible global function definition for ‘median’
Undefined global functions or variables:
  as.formula complete.cases covMcd frequency mad median na.omit nearcor
  posdefify residuals toeplitz
Consider adding
  importFrom("stats", "as.formula", "complete.cases", "frequency", "mad",
             "median", "na.omit", "residuals", "toeplitz")
to your NAMESPACE file.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'distrMod', 'ROptEst', 'distr', 'distrEx', 'RandVar', 'RobAStBase'

Package suggested but not available for checking: ‘ismev’

Package which this enhances but not available for checking: ‘fitdistrplus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/robfilter.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'doParallel', 'doRNG'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'leaflet', 'mapedit'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'distr', 'affy', 'Biobase', 'beadarray', 'RobLox', 'distrMod',
  'AnnotationDbi'

Packages suggested but not available for checking:
  'affydata', 'hgu95av2cdf', 'beadarrayExampleData',
  'illuminaHumanv3.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'distrMod', 'RobAStBase', 'Biobase', 'RandVar', 'distr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'BayesTools', 'rjags'

Packages suggested but not available for checking: 'rstan', 'metaBMA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'quantreg', 'sn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fastGHQuad', 'doParallel', 'doRNG'

Packages suggested but not available for checking: 'R.rsp', 'forward'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'flexmix', 'robust', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'markovchain', 'tm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘future.apply’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘quantreg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘GSE’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ROptRegTS', 'distr', 'RandVar', 'RobAStBase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
RobRSVD: no visible global function definition for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
Package suggested but not available for checking: ‘readr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘gallery.Rmd’ using rmarkdown
Quitting from lines 73-94 (gallery.Rmd) 
Error: processing vignette ‘gallery.Rmd’ failed with diagnostics:
there is no package called 'readr'
--- failed re-building ‘gallery.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
--- finished re-building ‘introduction.Rmd’

--- re-building ‘shiny.Rmd’ using rmarkdown
--- finished re-building ‘shiny.Rmd’

SUMMARY: processing the following file failed:
  ‘gallery.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘rrcov’

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Packages required but not available: 'AER', 'doRNG'

Packages suggested but not available for checking: 'doFuture', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RobustAFT.Rcheck/00install.out’ for details.
Package required but not available: ‘splusTimeSeries’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'robust', 'MPV', 'GGally', 'catdata', 'doParallel'

Packages which this enhances but not available for checking:
  'rrcov', 'quantreg', 'Hmisc'
Error(s) in re-building vignettes:
  ...
--- re-building ‘fastMcd-kmini.Rnw’ using Sweave
Loading required package: robustbase
--- finished re-building ‘fastMcd-kmini.Rnw’

--- re-building ‘lmrob_simulation.Rnw’ using Sweave
Loading required package: xtable
Loading required package: ggplot2
Loading required package: GGally
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘GGally’

Error: processing vignette ‘lmrob_simulation.Rnw’ failed with diagnostics:
 chunk 2 (label = graphics-setup) 
Error : require(GGally) is not TRUE

--- failed re-building ‘lmrob_simulation.Rnw’

--- re-building ‘psi_functions.Rnw’ using Sweave
--- finished re-building ‘psi_functions.Rnw’

SUMMARY: processing the following file failed:
  ‘lmrob_simulation.Rnw’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘rjags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'doParallel'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/robustDA.Rcheck/00install.out’ for details.
Package required but not available: ‘rrcov’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/robustgam.Rcheck/00install.out’ for details.
Found the following significant warnings:
  /usr/lib/gcc/x86_64-linux-gnu/12/include/emmintrin.h:131:24: warning: array subscript ‘__m128d_u[0]’ is partly outside array bounds of ‘Eigen::internal::plain_matrix_type<Eigen::Product<Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false>, Eigen::Transpose<Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false> >, 0>, Eigen::Dense>::type [1]’ {aka ‘Eigen::Matrix<double, 1, 1, 0, 1, 1> [1]’} [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RobustGaSP.Rcheck/00install.out’ for details.
Package required but not available: ‘perry’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lme4', 'fastGHQuad'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/robustrank.Rcheck/00install.out’ for details.
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rrcov’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MCMCpack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'robreg3S', 'GSE'

Package suggested but not available for checking: ‘systemfit’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘ICS’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rocc.Rcheck/00install.out’ for details.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Packages suggested but not available for checking: 'Hmisc', 'car', 'HH'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'RMariaDB', 'RPostgres', 'RSQLite'
Running examples in ‘rocker-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: appendTable
> ### Title: Append data to table.
> ### Aliases: appendTable
> 
> ### ** Examples
> 
> db <- rocker::newDB()
dctr | New object 
> rocker::setupSQLite(db)
Error: Package RSQLite not installed
Execution halted
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Package required but not available: ‘DiagrammeR’

Packages suggested but not available for checking:
  'haven', 'justifier', 'rENA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rockr.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'np', 'spatstat.geom', 'spatstat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ROCpsych.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ROCS.Rcheck/00install.out’ for details.
Package required but not available: ‘svmpath’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DiagrammeR', 'flexsurv'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rodam.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘fda.usc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rfast', 'TreeDist', 'TreeTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rglpk’
Packages required but not available: 'R.utils', 'Rglpk'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rglpk’
Package required but not available: ‘alabama’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcplex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rglpk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ROI.plugin.glpk’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ldaPrototype', 'tosca'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rolocISCCNBS.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘DiagrammeR’
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
  ...
--- re-building ‘rolog.Rmd’ using rmarkdown
Quitting from lines 14-19 (rolog.Rmd) 
Error: processing vignette ‘rolog.Rmd’ failed with diagnostics:
there is no package called 'DiagrammeR'
--- failed re-building ‘rolog.Rmd’

SUMMARY: processing the following file failed:
  ‘rolog.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RolWinMulCor.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘plotly’

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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/R.oo.Rcheck/00install.out’ for details.
Package required but not available: ‘doParallel’

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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ropensecretsapi.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'haven', 'readr', 'rio'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘CodeDepends’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'distr', 'distrEx', 'RandVar'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'distr', 'distrEx', 'distrMod', 'RandVar', 'RobAStBase'

Package suggested but not available for checking: ‘RobLox’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ROptEstOld', 'distr', 'distrEx', 'RandVar'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ROracle.Rcheck/00install.out’ for details.
Package required but not available: ‘Rglpk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'car', 'ggrepel', 'lme4', 'ufs', 'viridis'

Packages suggested but not available for checking: 'GGally', 'MBESS', 'rio'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rgdal’

Packages suggested but not available for checking: 'cartography', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'mrfDepth', 'rrcov', 'rrcovHD', 'elasticnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rotasym.Rcheck/00install.out’ for details.
Package required but not available: ‘sphereplot’

Package suggested but not available for checking: ‘onion’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GA', 'ftsa'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'MCMCglmm', 'phylobase', 'RNeXML'
Error(s) in re-building vignettes:
  ...
--- re-building ‘data_mashups.Rmd’ using rmarkdown
Quitting from lines 151-155 (data_mashups.Rmd) 
Error: processing vignette ‘data_mashups.Rmd’ failed with diagnostics:
there is no package called 'phylobase'
--- failed re-building ‘data_mashups.Rmd’

--- re-building ‘meta-analysis.Rmd’ using rmarkdown
--- finished re-building ‘meta-analysis.Rmd’

--- re-building ‘rotl.Rmd’ using rmarkdown
--- finished re-building ‘rotl.Rmd’

SUMMARY: processing the following file failed:
  ‘data_mashups.Rmd’

Error: Vignette re-building failed.
Execution halted
'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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RoughSets.Rcheck/00install.out’ for details.
Package required but not available: ‘geometry’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/roxut.Rcheck/00install.out’ for details.
Package required but not available: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'R.oo'
Running ‘testthat.R’ [16s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(roxygen2)
  > 
  > if (requireNamespace("xml2")) {
  +   test_check("roxygen2", reporter = MultiReporter$new(reporters = list(JunitReporter$new(file = "test-results.xml"), CheckReporter$new())))
  + } else {
  +   test_check("roxygen2")
  + }
  [WARNING] Duplicate link reference '[roxygenize()]' at line 8 column 1
  [WARNING] Duplicate link reference '[stringr::str_length()]' at line 9 column 1
  [ FAIL 1 | WARN 5 | SKIP 16 | PASS 729 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (13)
  • devtools cannot be loaded (2)
  • file.exists(test_path("../../DESCRIPTION")) is not TRUE (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-object-from-call.R:182:3): can define constructor with R.oo ─────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'R.oo'
  Backtrace:
      ▆
   1. ├─roxygen2:::call_to_object(...) at test-object-from-call.R:182:2
   2. │ └─base::eval(code, envir = env)
   3. │   └─base::eval(code, envir = env)
   4. └─base::loadNamespace(x) at test-object-from-call.R:183:4
   5.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   6.     └─base withOneRestart(expr, restarts[[1L]])
   7.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 5 | SKIP 16 | PASS 729 ]
  Error: Test failures
  Execution halted
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.
Package required but not available: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘truncdist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'agricolae'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'picante', 'bipartite', 'fields', 'fpc', 'mvMORPH', 'phytools',
  'raster', 'Rmpfr', 'TESS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'geoR', 'RandomFields'
Package required but not available: ‘Seurat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rpart.LAD.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘earth’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rpart.plot.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rpartScore.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rpart.utils.Rcheck/00install.out’ for details.
Package required but not available: ‘np’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘xlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rpdb.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RpeakChrom.Rcheck/00install.out’ for details.
Package required but not available: ‘RPEIF’

Packages suggested but not available for checking:
  'R.rsp', 'PerformanceAnalytics'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xts', 'RobStatTM'

Packages suggested but not available for checking:
  'R.rsp', 'PerformanceAnalytics'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RPEnsemble.Rcheck/00install.out’ for details.
Packages required but not available:
  'xts', 'RPEIF', 'RPEGLMEN', 'RobStatTM'

Packages suggested but not available for checking:
  'R.rsp', 'PerformanceAnalytics'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mirt’
Running ‘testthat.R’ [5s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rpf)
  Loading required package: parallel
  > 
  > test_check("rpf")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 382 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-mirt-icc.R:4:1): (code run outside of `test_that()`) ────────────
  <packageNotFoundError/error/condition>
  Error in `library(mirt)`: there is no package called 'mirt'
  Backtrace:
      ▆
   1. └─base::library(mirt) at test-mirt-icc.R:4:0
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 382 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rphylip.Rcheck/00install.out’ for details.
Packages required but not available:
  'doBy', 'geiger', 'phylolm', 'phytools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘devtools’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rplotengine.Rcheck/00install.out’ for details.
Package required but not available: ‘rbacon’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RPMM.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘geometry’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘xts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘truncdist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RPostgreSQL', 'raster', 'rgeos'

Packages suggested but not available for checking: 'RPostgres', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RPostgreSQL.Rcheck/00install.out’ for details.
Package required but not available: ‘bit64’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rPowerSampleSize.Rcheck/00install.out’ for details.
Packages required but not available: 'quantreg', 'gam', 'Hmisc', 'Biobase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'doParallel', 'imager', 'cobs', 'quantreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gamlss.dist', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'dygraphs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dygraphs', 'quantmod', 'xts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'graph', 'Rgraphviz'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Packages suggested but not available for checking:
  'flexsurv', 'flexsurvcure', 'rms'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rprev.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘readr’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘multiple-files.Rmd’ using rmarkdown
--- finished re-building ‘multiple-files.Rmd’

--- re-building ‘parsing-summary.Rmd’ using rmarkdown
--- finished re-building ‘parsing-summary.Rmd’

--- re-building ‘quick-start-demo.Rmd’ using rmarkdown
Quitting from lines 141-148 (quick-start-demo.Rmd) 
Error: processing vignette ‘quick-start-demo.Rmd’ failed with diagnostics:
there is no package called 'readr'
--- failed re-building ‘quick-start-demo.Rmd’

SUMMARY: processing the following file failed:
  ‘quick-start-demo.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘viridis’

Package suggested but not available for checking: ‘mlogit’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘sqldf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tableone’
Package required but not available: ‘geomorph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggpubr’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘Rpvt.Rmd’ using rmarkdown
Quitting from lines 115-172 (Rpvt.Rmd) 
Error: processing vignette ‘Rpvt.Rmd’ failed with diagnostics:
there is no package called 'ggpubr'
--- failed re-building ‘Rpvt.Rmd’

SUMMARY: processing the following file failed:
  ‘Rpvt.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘raster’

Package suggested but not available for checking: ‘spData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rquery’

Package suggested but not available for checking: ‘RSQLite’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘itertools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘quantreg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘GEOmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘RQuantLib-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SabrSwaption
> ### Title: SABR swaption using vol cube data with bermudan alternative
> ###   using markovfunctional
> ### Aliases: SabrSwaption SabrSwaption.default
> ### Keywords: models
> 
> ### ** Examples
> 
> 
> params <- list(tradeDate=as.Date('2016-2-15'),
+                settleDate=as.Date('2016-2-17'),
+                startDate=as.Date('2017-2-17'),
+                maturity=as.Date('2022-2-17'),
+                european=TRUE,
+                dt=.25,
+                expiryDate=as.Date('2017-2-17'),
+                strike=.02,
+                interpWhat="discount",
+                interpHow="loglinear")
> 
> # Set leg paramters for generating discount curve
> dclegparams=list(dayCounter="Thirty360",
+                  fixFreq="Annual",
+                  floatFreq="Semiannual")
> 
> setEvaluationDate(as.Date("2016-2-16"))               
[1] TRUE
> times<-times <- seq(0,14.75,.25)
> 
> data(tsQuotes)
> dcurve <- DiscountCurve(params, tsQuotes, times=times,dclegparams)
Error in discountCurveEngine(params, tsQuotes, times, matchlegs) : 
  1st iteration: failed at 1st alive instrument, pillar March 17th, 2016, maturity March 17th, 2016, reference date February 17th, 2016: Missing no-fix1M Actual/360 fixing for February 15th, 2016
Calls: DiscountCurve -> DiscountCurve.default -> discountCurveEngine
Execution halted
Packages suggested but not available for checking: 'RSQLite', 'rqdatatable'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rquery.Rcheck/00install.out’ for details.
Packages required but not available: 'lme4', 'phylolm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘diagram’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rRAP.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘HL_H0.pdf’ ‘pi0infer.pdf’ ‘rate.txt’ ‘summary.txt’
Package required but not available: ‘quantreg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'warbleR', 'NatureSounds'

Package suggested but not available for checking: ‘vegan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RobStatTM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rrcov’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rrcov', 'robustHD'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rrcov’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rrcov.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rrecsys.Rcheck/00install.out’ for details.
Package required but not available: ‘RPostgreSQL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xlsx', 'doSNOW'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (7) combine.Rd:31: invalid email address: andy\_liaw@merck.com
checkRd: (7) getTree.Rd:55: invalid email address: andy\_liaw@merck.com
checkRd: (7) grow.Rd:37: invalid email address: andy\_liaw@merck.com
checkRd: (7) partialPlot.Rd:79: invalid email address: andy\_liaw@merck.com
checkRd: (7) predict.RRF.Rd:82: invalid email address: andy\_liaw@merck.com
checkRd: (7) predict.RRF.Rd:83: invalid email address: matthew\_wiener@merck.com
checkRd: (7) treesize.Rd:34: invalid email address: andy\_liaw@merck.com
checkRd: (7) varImpPlot.Rd:37: invalid email address: andy\_liaw@merck.com
'LazyData' is specified without a 'data' directory
Packages required but not available: 'mc2d', 'msm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rrpack’
Error(s) in re-building vignettes:
  ...
--- re-building ‘rrMixture.Rmd’ using rmarkdown
Loading required package: rrpack
Quitting from lines 256-264 (rrMixture.Rmd) 
Error: processing vignette ‘rrMixture.Rmd’ failed with diagnostics:
could not find function "rrr"
--- failed re-building ‘rrMixture.Rmd’

SUMMARY: processing the following file failed:
  ‘rrMixture.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘test.bpl’ ‘test.cr’ ‘test.ct’
Package suggested but not available for checking: ‘biwavelet’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'phytools', 'geiger', 'doParallel'

Packages suggested but not available for checking:
  'phangorn', 'R.utils', 'car', 'picante', 'vegan', 'ddpcr',
  'geomorph', 'mvMORPH', 'Morpho', 'evolqg', 'webshot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arm', 'magic'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'lme4'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'GGally'

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘expm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'R.oo', 'R.utils', 'R.cache'

Package suggested but not available for checking: ‘R.devices’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'editData', 'ggpubr', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rrum.Rcheck/00install.out’ for details.
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.
Packages required but not available: 'dendextend', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'stars', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gstat', 'shapefiles', 'rgdal'

Packages suggested but not available for checking: 'maptools', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'hydroGOF', 'cvTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘SNPRelate’

Packages suggested but not available for checking:
  'plotly', 'biomaRt', 'raster', 'spdep', 'rgdal', 'gdalUtils',
  'rworldmap', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘furrr’

Package suggested but not available for checking: ‘recipes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'fields', 'qgraph'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RSA.Rcheck/00install.out’ for details.
Package required but not available: ‘arules’

Package suggested but not available for checking: ‘MultiOrd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'leafem', 'leaflet', 'tmap', 'fields', 'calendR', 'raster', 'stars'

Package suggested but not available for checking: ‘rgdal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rgdal’
stripslash: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RSauceLabs.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘devtools’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RSCAT.Rcheck/00install.out’ for details.
Package required but not available: ‘tm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘seqinr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘RScelestial-vignette.Rmd’ using rmarkdown
Quitting from lines 84-86 (RScelestial-vignette.Rmd) 
Error: processing vignette ‘RScelestial-vignette.Rmd’ failed with diagnostics:
there is no package called 'seqinr'
--- failed re-building ‘RScelestial-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘RScelestial-vignette.Rmd’

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
'LazyData' is specified without a 'data' directory
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggpolypath', 'glmnet', 'FactoMineR', 'sqldf', 'labelled'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rSEA.Rcheck/00install.out’ for details.
Packages required but not available: 'sybil', 'RBGL', 'graph'

Package suggested but not available for checking: ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (7) distseisnXY.Rd:18: \item in \value must have non-empty label
checkRd: (7) distseisnXY.Rd:19: \item in \value must have non-empty label
Package suggested but not available for checking: ‘Rcompression’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rsem.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
  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’

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.
Package suggested but not available for checking: ‘ggraph’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Categorical-and-continuous-features.Rmd’ using rmarkdown

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union


Attaching package: 'dplyr'

The following objects are masked from 'package:igraph':

    as_data_frame, groups, union

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 20-24 (Categorical-and-continuous-features.Rmd) 
Error: processing vignette ‘Categorical-and-continuous-features.Rmd’ failed with diagnostics:
there is no package called 'ggraph'
--- failed re-building ‘Categorical-and-continuous-features.Rmd’

--- re-building ‘separate-peels-quintet.Rmd’ using rmarkdown

Attaching package: 'tidyr'

The following object is masked from 'package:igraph':

    crossing


Attaching package: 'purrr'

The following objects are masked from 'package:igraph':

    compose, simplify

Quitting from lines 28-35 (separate-peels-quintet.Rmd) 
Error: processing vignette ‘separate-peels-quintet.Rmd’ failed with diagnostics:
there is no package called 'ggraph'
--- failed re-building ‘separate-peels-quintet.Rmd’

SUMMARY: processing the following files failed:
  ‘Categorical-and-continuous-features.Rmd’
  ‘separate-peels-quintet.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘MCMCpack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sn', 'RSQLite', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'rstpm2'
Error(s) in re-building vignettes:
  ...
--- re-building ‘A-introduction.Rmd’ using rmarkdown
--- finished re-building ‘A-introduction.Rmd’

--- re-building ‘B-relhaz.Rmd’ using rmarkdown
Quitting from lines 160-185 (B-relhaz.Rmd) 
Error: processing vignette ‘B-relhaz.Rmd’ failed with diagnostics:
there is no package called 'rstpm2'
--- failed re-building ‘B-relhaz.Rmd’

--- re-building ‘C-plotting.Rmd’ using rmarkdown
--- finished re-building ‘C-plotting.Rmd’

--- re-building ‘D-nlp.Rmd’ using rmarkdown
--- finished re-building ‘D-nlp.Rmd’

--- re-building ‘E-custom-inputs.Rmd’ using rmarkdown
--- finished re-building ‘E-custom-inputs.Rmd’

--- re-building ‘F-rsimsumtidyverse.Rmd’ using rmarkdown
--- finished re-building ‘F-rsimsumtidyverse.Rmd’

SUMMARY: processing the following file failed:
  ‘B-relhaz.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'aire.zmvm', 'mapproj', 'ggmap', 'gstat'
Packages required but not available: 'raster', 'rgdal', 'rasterVis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘flexclust’

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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mlxR’
Packages suggested but not available for checking: 'DoE.base', 'FrF2'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RSNNS.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘readr’
Package suggested but not available for checking: ‘editrules’
Packages required but not available: 'spatialEco', 'tigris', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘MatrixExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Skipping vignette re-building
Packages suggested but not available for checking:
  'R.rsp', 'INLA', 'rgdal', 'splancs', 'fields'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rSPDE.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RSQLite', 'disk.frame'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bit64’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RSQLite’
Running examples in ‘RSQL-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RSQL
> ### Title: rsql
> ### Aliases: RSQL .onLoad
> 
> ### ** Examples
> 
> library(RSQL)
> library(RSQLite)
Error in library(RSQLite) : there is no package called ‘RSQLite’
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DBI)
  > library(RSQLite)
  Error in library(RSQLite) : there is no package called 'RSQLite'
  Execution halted
Packages required but not available: 'SIS', 'GMMAT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'EcoHydRology', 'gsubfn', 'qmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RsSimulx.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lme4', 'rstan', 'shinystan'

Packages suggested but not available for checking: 'biglm', 'betareg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shinystan’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rstan.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rstan’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘car’

Packages suggested but not available for checking: 'ggpubr', 'coin'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'raster', 'caret', 'rgdal', 'exactextractr', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RStorm.Rcheck/00install.out’ for details.
Package required but not available: ‘xslt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fastGHQuad’

Package suggested but not available for checking: ‘mstate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggrepel’

Package suggested but not available for checking: ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rsubgroup.Rcheck/00install.out’ for details.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rsurfer.Rcheck/00install.out’ for details.
Packages required but not available: 'epiR', 'mc2d'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'inlmisc', 'raster', 'rgdal', 'rgeos'

Package suggested but not available for checking: ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pcaMethods’
Error(s) in re-building vignettes:
  ...
--- re-building ‘rSVDdpd-intro.Rmd’ using rmarkdown
Quitting from lines 19-23 (rSVDdpd-intro.Rmd) 
Error: processing vignette ‘rSVDdpd-intro.Rmd’ failed with diagnostics:
there is no package called 'pcaMethods'
--- failed re-building ‘rSVDdpd-intro.Rmd’

SUMMARY: processing the following file failed:
  ‘rSVDdpd-intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Package vignette with placeholder title ‘Vignette Title’:
  ‘vignette.Rmd’
Found the following files/directories:
  ‘mapCH2017.rda’
Packages required but not available: 'RSQLite', 'raster'

Package suggested but not available for checking: ‘rgdal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rTableICC.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rtables.Rcheck/00install.out’ for details.
Package required but not available: ‘vegan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Package suggested but not available for checking: ‘rgeos’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tseries’
Running ‘test-EPD.R’ [1s/2s]
  Running ‘test-EUstockmarket.R’ [0s/1s]
  Running ‘test-FGM.R’ [2s/3s]
  Running ‘test-MDPD.R’ [0s/1s]
  Running ‘test-RTDE.R’ [2s/3s]
  Running ‘test-dataRTDE.R’ [0s/1s]
  Running ‘test-fitRTDE.R’ [2s/4s]
  Running ‘test-frank.R’ [0s/1s]
  Running ‘test-frechet.R’ [0s/1s]
  Running ‘test-multRTDE.R’ [6s/10s]
  Running ‘test-zvalue.R’ [0s/1s]
Running the tests in ‘tests/test-EUstockmarket.R’ failed.
Complete output:
  > data(EuStockMarkets)
  > 
  > 
  > library(RTDE)
  Loading required package: parallel
  > library(tseries)
  Error in library(tseries) : there is no package called 'tseries'
  Execution halted
Package required but not available: ‘msm’

Package suggested but not available for checking: ‘latticeExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tm', 'FactoMineR', 'wordcloud', 'tm.plugin.factiva',
  'tm.plugin.lexisnexis', 'tm.plugin.europresse', 'tm.plugin.alceste'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rNOMADS’
Package required but not available: ‘RSQLite’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tm', 'ipred', 'glmnet'

See section ‘The DESCRIPTION file’ 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.
Package required but not available: ‘R.oo’

Package suggested but not available for checking: ‘gsubfn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘brnn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Packages required but not available: 'readr', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DescTools', 'lme4'

Packages suggested but not available for checking: 'devtools', 'sjPlot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'GenomicRanges', 'GenomeInfoDb', 'TailRank', 'IRanges'

Packages suggested but not available for checking: 'Gviz', 'rtracklayer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rtip.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rtkore.Rcheck/00install.out’ for details.
Packages required but not available:
  'feasts', 'plotly', 'readr', 'tidyquant', 'timetk', 'xts'

Packages suggested but not available for checking:
  'PerformanceAnalytics', 'Quandl', 'rgdal', 'rugarch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'alphashape3d', 'doSNOW', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'GEOmap', 'splancs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gstat’

Packages suggested but not available for checking:
  'intamap', 'rgeos', 'spacetime', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Hmisc', 'raster', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘future.apply’

Packages suggested but not available for checking:
  'quantmod', 'vars', 'xts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'leaflet', 'showtext'
Package suggested but not available for checking: ‘geometry’
Running ‘attributes.R’ [0s/1s]
  Comparing ‘attributes.Rout’ to ‘attributes.Rout.save’ ... OK
  Running ‘basic.R’ [0s/1s]
  Comparing ‘basic.Rout’ to ‘basic.Rout.save’ ... OK
  Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("RTriangle")
  Loading required package: RTriangle
  [ FAIL 2 | WARN 1 | SKIP 2 | PASS 8 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • empty test (2)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-triangulate.R:16:3): triangulate can trianglulate a square ──────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'geometry'
  Backtrace:
      ▆
   1. ├─RTriangle tri.area(tp$P, tp$T) at test-triangulate.R:16:2
   2. └─base::loadNamespace(x) at test-triangulate.R:9:2
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base withOneRestart(expr, restarts[[1L]])
   5.       └─base doWithOneRestart(return(expr), restart)
  ── Error (test-triangulate.R:31:3): triangulate can trianglulate an object with a concavity subject to a minimum area constraint ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'geometry'
  Backtrace:
      ▆
   1. ├─RTriangle tri.area(tp$P, tp$T) at test-triangulate.R:31:2
   2. └─base::loadNamespace(x) at test-triangulate.R:9:2
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base withOneRestart(expr, restarts[[1L]])
   5.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 1 | SKIP 2 | PASS 8 ]
  Error: Test failures
  Execution halted
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Errors in running code in vignettes:
when running code in ‘Skylark_example.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?
when running code in ‘rtrim_2_extensions.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?
when running code in ‘rtrim_confidence_intervals.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?
when running code in ‘rtrim_for_TRIM_users.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?
when running code in ‘taming_overdispersion.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘Skylark_example.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘rtrim_2_extensions.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘rtrim_confidence_intervals.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘rtrim_for_TRIM_users.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘taming_overdispersion.Rmd’ using ‘UTF-8’... failed to complete the test
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
GNU make is a SystemRequirements.
Errors in running code in vignettes:
when running code in ‘mcMat.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?
when running code in ‘rTRNG.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘mcMat.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘rTRNG.Rmd’ using ‘UTF-8’... failed to complete the test
Packages required but not available: 'Rfast', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rstan’

Package suggested but not available for checking: ‘cmdstanr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xts', 'quantmod', 'Quandl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘irlba’
Running ‘testthat.R’ [8s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("Rtsne")
  Loading required package: Rtsne
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 38 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (2)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_Rtsne.R:141:3): partial_pca FALSE and TRUE give similar results ──
  Error: Package "irlba" is required for partial PCA. Please install it.
  Backtrace:
      ▆
   1. ├─Rtsne::Rtsne(fat_data, partial_pca = T, max_iter = iter_equal) at test_Rtsne.R:141:2
   2. └─Rtsne:::Rtsne.default(fat_data, partial_pca = T, max_iter = iter_equal)
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 38 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'xts', 'quantmod'

Package suggested but not available for checking: ‘TTR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xts', 'raster'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RStoolbox', 'moveVis', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘Tsttwalk.dat’
Package suggested but not available for checking: ‘readr’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rucm.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘dtw’
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_rucrdtw.Rmd’ using rmarkdown
Quitting from lines 95-100 (using_rucrdtw.Rmd) 
Error: processing vignette ‘using_rucrdtw.Rmd’ failed with diagnostics:
there is no package called 'dtw'
--- failed re-building ‘using_rucrdtw.Rmd’

SUMMARY: processing the following file failed:
  ‘using_rucrdtw.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ks', 'xts'

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
Package required but not available: ‘dials’

Packages suggested but not available for checking:
  'C50', 'Cubist', 'recipes', 'xrf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'maxLik', 'highfrequency', 'xts', 'tseries'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyverse’

Package suggested but not available for checking: ‘tidymodels’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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’
Packages suggested but not available for checking: 'rjags', 'modeest'
'LazyData' is specified without a 'data' directory
checkRd: (7) Runuran-package.Rd:38-40: \item in \describe must have non-empty label
checkRd: (7) Runuran-package.Rd:41-44: \item in \describe must have non-empty label
checkRd: (7) Runuran-package.Rd:45-49: \item in \describe must have non-empty label
checkRd: (7) Runuran-package.Rd:50-52: \item in \describe must have non-empty label
Package required but not available: ‘taxize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggforce’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘R.utils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘R.utils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘R.oo’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RUVIIIC.Rcheck/00install.out’ for details.
Packages required but not available:
  'car', 'FactoMineR', 'lme4', 'mixOmics', 'vegan'

Packages suggested but not available for checking:
  'betareg', 'FSA', 'glmmTMB', 'labdsv'

Package which this enhances but not available for checking: ‘glmmADMB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'GSVAdata', 'clusterProfiler', 'edgeR', 'org.Hs.eg.db',
  'ComplexHeatmap', 'GSEABase', 'ggpubr', 'haven', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Morpho’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RVCompare.Rcheck/00install.out’ for details.
Packages required but not available: 'ggforce', 'vegan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘readr’
Packages required but not available: 'coxme', 'lme4', 'kinship2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rvHPDT.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RVideoPoker.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘gpuR’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rviewgraph.Rcheck/00install.out’ for details.
Package required but not available: ‘kde1d’

Package suggested but not available for checking: ‘ggraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RVowpalWabbit.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rvTDT.Rcheck/00install.out’ for details.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plotly’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘imager’
Error(s) in re-building vignettes:
  ...
--- re-building ‘rwaveletvignette.Rmd’ using rmarkdown
Quitting from lines 173-183 (rwaveletvignette.Rmd) 
Error: processing vignette ‘rwaveletvignette.Rmd’ failed with diagnostics:
a dimension is zero
--- failed re-building ‘rwaveletvignette.Rmd’

SUMMARY: processing the following file failed:
  ‘rwaveletvignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘rgdal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lsa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘xts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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’
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘partykit’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'biglm', 'arm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘marked’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'gdistance'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘raster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘raster’
Package suggested but not available for checking: ‘jiebaR’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rwordseg.Rcheck/00install.out’ for details.
Packages required but not available: 'maptools', 'fields'

Packages suggested but not available for checking: 'rgdal', 'rworldxtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rworldmap’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rworldxtra.Rcheck/00install.out’ for details.
Package required but not available: ‘sos’

Package suggested but not available for checking: ‘cranly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
.dwt: no visible global function definition for ‘median’
.udwt: no visible global function definition for ‘median’
plotSignalTransformation: no visible global function definition for
  ‘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.
Package suggested but not available for checking: ‘bfast’
Packages required but not available: 'phangorn', 'viridis', 'GGally'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘MCMCpack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘kappalab’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rcdk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggrepel', 'xgxr', 'devtools'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rxSeq.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RXshrink.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘devtools’
Packages suggested but not available for checking: 'devtools', 'Rmpfr'
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RYoudaoTranslate.Rcheck/00install.out’ for details.
Package required but not available: ‘car’

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
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GEOmap', 'mapproj'

Package suggested but not available for checking: ‘easyVerification’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'mapproj', 'ClimProjDiags', 'multiApply', 'easyNCDF'

Package suggested but not available for checking: ‘easyVerification’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘glmnet’
Error(s) in re-building vignettes:
  ...
--- re-building ‘supervised.Rmd’ using rmarkdown
Warning in predict.lm(lm.fit, data.frame(train$xL)) :
  prediction from a rank-deficient fit may be misleading
Quitting from lines 69-84 (supervised.Rmd) 
Error: processing vignette ‘supervised.Rmd’ failed with diagnostics:
there is no package called 'glmnet'
--- failed re-building ‘supervised.Rmd’

SUMMARY: processing the following file failed:
  ‘supervised.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'biclust', 'irlba'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/saasCNV.Rcheck/00install.out’ for details.
Package required but not available: ‘raster’

Package which this enhances but not available for checking: ‘stars’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Trading’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘DDD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'PDQutils', 'orthopolynom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sad.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘vegan’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sads.Rcheck/00install.out’ for details.
Package required but not available: ‘sae’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘COUNT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rjags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rjags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rjags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rjags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rjags', 'CARBayesdata'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rjags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rjags’

Package suggested but not available for checking: ‘saeHB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rjags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rjags’

Package suggested but not available for checking: ‘saeHB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/saemix.Rcheck/00install.out’ for details.
Package required but not available: ‘smallarea’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘spdep’

Packages suggested but not available for checking: 'sae', 'saeSim'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
fit.saery.AR1: no visible global function definition for ‘qnorm’
fit.saery.MA1: no visible global function definition for ‘qnorm’
fit.saery.indep: no visible global function definition for ‘qnorm’
mse.saery.boot.AR1.typeI: no visible global function definition for
  ‘rnorm’
mse.saery.boot.AR1.typeI: no visible global function definition for
  ‘write.table’
mse.saery.boot.AR1.typeII: no visible global function definition for
  ‘rnorm’
mse.saery.boot.AR1.typeII: no visible global function definition for
  ‘write.table’
mse.saery.boot.MA1.typeI: no visible global function definition for
  ‘rnorm’
mse.saery.boot.MA1.typeI: no visible global function definition for
  ‘write.table’
mse.saery.boot.MA1.typeII: no visible global function definition for
  ‘rnorm’
mse.saery.boot.MA1.typeII: no visible global function definition for
  ‘write.table’
plot.saery: no visible global function definition for ‘devAskNewPage’
plot.saery: no visible global function definition for ‘par’
plot.saery: no visible global function definition for ‘abline’
plot.saery: no visible global function definition for ‘title’
plot.saery: no visible global function definition for ‘axis’
plot.saery: no visible global function definition for ‘lines’
plot.saery: no visible global function definition for ‘legend’
pvalue: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline axis devAskNewPage legend lines par pnorm qnorm rnorm title
  write.table
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "title")
  importFrom("stats", "pnorm", "qnorm", "rnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Package required but not available: ‘spdep’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lmtest', 'car', 'ggspatial'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/safeBinaryRegression.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'plotly', 'Tendril'

Package suggested but not available for checking: ‘safetyGraphics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'datamods', 'safetyCharts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'PMCMRplus', 'devtools', 'DescTools', 'GGally', 'car',
  'ggiraphExtra', 'spatstat', 'vcd'
Package required but not available: ‘MixSim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘glmnet’
Running examples in ‘sAIC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sAIC
> ### Title: Compute the Akaike information criterion for the lasso in
> ###   generalized linear models
> ### Aliases: sAIC
> ### Keywords: models regression
> 
> ### ** Examples
> 
> library(MASS)
> library(glmnet)
Error in library(glmnet) : there is no package called ‘glmnet’
Execution halted
Package required but not available: ‘glmnet’

Package suggested but not available for checking: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SALES.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SALTSampler.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘survey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'gdistance', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'maxLik', 'systemfit'

Packages suggested but not available for checking: 'lmtest', 'Ecdat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘TeachingSampling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DescTools’
Error(s) in re-building vignettes:
  ...
--- re-building ‘samplesizeCMH-introduction.Rmd’ using rmarkdown
Quitting from lines 136-139 (samplesizeCMH-introduction.Rmd) 
Error: processing vignette ‘samplesizeCMH-introduction.Rmd’ failed with diagnostics:
there is no package called 'DescTools'
--- failed re-building ‘samplesizeCMH-introduction.Rmd’

--- re-building ‘samplesizeCMH-power.Rmd’ using rmarkdown
--- finished re-building ‘samplesizeCMH-power.Rmd’

--- re-building ‘samplesizeCMH-samplesize.Rmd’ using rmarkdown
--- finished re-building ‘samplesizeCMH-samplesize.Rmd’

SUMMARY: processing the following file failed:
  ‘samplesizeCMH-introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/samplesizelogisticcasecontrol.Rcheck/00install.out’ for details.
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.
Packages suggested but not available for checking: 'haven', 'rio'
Package required but not available: ‘survey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rnw’ using knitr
Quitting from lines 819-822 (my-vignette.Rnw) 
Error: processing vignette ‘my-vignette.Rnw’ failed with diagnostics:
there is no package called 'lme4'
--- failed re-building ‘my-vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘my-vignette.Rnw’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/samplingEstimates.Rcheck/00install.out’ for details.
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'latticeExtra', 'rasterVis'

Package suggested but not available for checking: ‘rgeos’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'MSEtool', 'snowfall', 'vars'

Packages suggested but not available for checking: 'caret', 'tmbstan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘BART’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘metafor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RLumModel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'GO.db', 'GOstats', 'car', 'ergm', 'networkDynamic',
  'networkTomography', 'ngspatial', 'org.Sc.sgd.db', 'sna', 'vioplot'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sand.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'AER', 'car', 'lmtest', 'plm', 'strucchange'
Running ‘vcovCL.R’ [88s/128s]
  Comparing ‘vcovCL.Rout’ to ‘vcovCL.Rout.save’ ... OK
  Running ‘vcovPC.R’ [5s/8s]
  Comparing ‘vcovPC.Rout’ to ‘vcovPC.Rout.save’ ... OK
  Running ‘vcovPL.R’ [1s/1s]
Running the tests in ‘tests/vcovPL.R’ failed.
Complete output:
  > library("sandwich")
  > data("PetersenCL", package = "sandwich")
  > m <- lm(y ~ x, data = PetersenCL)
  > 
  > vcovPL(m, cluster = ~ firm + year, adjust = TRUE)
               (Intercept)            x
  (Intercept) 5.935164e-04 2.222292e-05
  x           2.222292e-05 7.934905e-04
  > vcovPL(m, cluster = ~ firm + year, adjust = FALSE)
               (Intercept)            x
  (Intercept) 5.932790e-04 2.221403e-05
  x           2.221403e-05 7.931731e-04
  > 
  > 
  > data("InstInnovation", package = "sandwich")
  > n <- glm(cites ~ institutions, family = poisson, data = InstInnovation)
  > 
  > vcovPL(n, cluster = ~ industry, adjust = TRUE)
                (Intercept)  institutions
  (Intercept)   0.095136753 -1.242281e-03
  institutions -0.001242281  2.129094e-05
  > vcovPL(n, cluster = ~ industry, adjust = FALSE)
                (Intercept)  institutions
  (Intercept)   0.095106103 -1.241881e-03
  institutions -0.001241881  2.128408e-05
  > 
  > 
  > ## vcovPL covariance matrix compared with vcovSCC from plm package
  > pm <- plm::plm(y ~ x, data = PetersenCL, model = "pooling", indexes = c("firm", "year"))
  Error in loadNamespace(x) : there is no package called 'plm'
  Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Errors in running code in vignettes:
when running code in ‘sandwich-CL.Rnw’
  ...

> library("sandwich")

> library("geepack")

> library("lattice")

> library("lmtest")

  When sourcing ‘sandwich-CL.R’:
Error: there is no package called ‘lmtest’
Execution halted
when running code in ‘sandwich-OOP.Rnw’
  ...

> library("AER")

  When sourcing ‘sandwich-OOP.R’:
Error: there is no package called ‘AER’
Execution halted
when running code in ‘sandwich.Rnw’
  ...

> library("zoo")

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric


> library("sandwich")

> library("strucchange")

  When sourcing ‘sandwich.R’:
Error: there is no package called ‘strucchange’
Execution halted

  ‘sandwich-CL.Rnw’... failed
  ‘sandwich-OOP.Rnw’... failed
  ‘sandwich.Rnw’... failed
Error(s) in re-building vignettes:
  ...
--- re-building ‘sandwich-CL.Rnw’ using Sweave

Error: processing vignette ‘sandwich-CL.Rnw’ failed with diagnostics:
 chunk 1 (label = preliminaries) 
Error in library("lmtest") : there is no package called ‘lmtest’

--- failed re-building ‘sandwich-CL.Rnw’

--- re-building ‘sandwich-OOP.Rnw’ using Sweave

Error: processing vignette ‘sandwich-OOP.Rnw’ failed with diagnostics:
 chunk 1 (label = preliminaries) 
Error in library("AER") : there is no package called ‘AER’

--- failed re-building ‘sandwich-OOP.Rnw’

--- re-building ‘sandwich.Rnw’ using Sweave

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric


Error: processing vignette ‘sandwich.Rnw’ failed with diagnostics:
 chunk 1 (label = preliminaries) 
Error in library("strucchange") : 
  there is no package called ‘strucchange’

--- failed re-building ‘sandwich.Rnw’

SUMMARY: processing the following files failed:
  ‘sandwich-CL.Rnw’ ‘sandwich-OOP.Rnw’ ‘sandwich.Rnw’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'geodetector', 'caret'

Package suggested but not available for checking: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readr', 'odbc'

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
Packages required but not available: 'doParallel', 'pcaMethods'

Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'bit64', 'haven'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggraph', 'ldatuning', 'topicmodels'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘furrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘openair’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'FitARMA', 'fGarch', 'fImport', 'forecast'
Error(s) in re-building vignettes:
  ...
--- re-building ‘garch_tests_example.Rnw’ using Sweave
Loading required package: stats4

Attaching package: ‘sarima’

The following object is masked from ‘package:stats’:

    spectrum


Error: processing vignette ‘garch_tests_example.Rnw’ failed with diagnostics:
 chunk 2 (label = setup) 
Error in library("fImport") : there is no package called ‘fImport’

--- failed re-building ‘garch_tests_example.Rnw’

--- re-building ‘white_noise_tests.Rnw’ using Sweave
--- finished re-building ‘white_noise_tests.Rnw’

SUMMARY: processing the following file failed:
  ‘garch_tests_example.Rnw’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘car’

Package suggested but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SARP.moodle.Rcheck/00install.out’ for details.
Package required but not available: ‘dtw’

Packages suggested but not available for checking: 'dendextend', 'smacof'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘sarp.snowprofile.alignment’
Packages required but not available: 'AzureRMR', 'AzureStor'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'AICcmodavg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
download.sas7bdat.sources : <anonymous>: no visible global function
  definition for ‘download.file’
generate.sas7bdat.source: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
Package required but not available: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sasLM.Rcheck/00install.out’ for details.
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Usinglmer.Rnw’ using Sweave

Error: processing vignette ‘Usinglmer.Rnw’ failed with diagnostics:
 chunk 1 (label = preliminaries) 
Error in library(lme4) : there is no package called ‘lme4’

--- failed re-building ‘Usinglmer.Rnw’

SUMMARY: processing the following file failed:
  ‘Usinglmer.Rnw’

Error: Vignette re-building failed.
Execution halted
GNU make is a SystemRequirements.
Package required but not available: ‘libr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Invalid NAMESPACE file, parsing gives:
Error in packageVersion("raster"): there is no package called ‘raster’

See section ‘Package namespaces’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'maptools', 'splancs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘SeerMapper’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'glmnet', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
loads: no visible global function definition for ‘untar’
saves: no visible global function definition for ‘tar’
Undefined global functions or variables:
  tar untar
Consider adding
  importFrom("utils", "tar", "untar")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/saws.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'MSGARCH', 'forecast', 'rugarch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'twang', 'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'poLCA', 'R.oo', 'flexmix'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘expm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘prodlim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (7) assess.Rd:23: \item in \describe must have non-empty label
checkRd: (7) assess.Rd:24: \item in \describe must have non-empty label
checkRd: (7) assess.Rd:25: \item in \describe must have non-empty label
checkRd: (7) assess.Rd:26: \item in \describe must have non-empty label
checkRd: (7) assess.Rd:27: \item in \describe must have non-empty label
checkRd: (7) assess.Rd:28: \item in \describe must have non-empty label
checkRd: (7) assess.Rd:29: \item in \describe must have non-empty label
checkRd: (7) assess.Rd:30: \item in \describe must have non-empty label
checkRd: (7) assess.Rd:31: \item in \describe must have non-empty label
checkRd: (7) assess.Rd:32: \item in \describe must have non-empty label
checkRd: (7) assess.Rd:33: \item in \describe must have non-empty label
checkRd: (7) sboost.Rd:26: \item in \describe must have non-empty label
checkRd: (7) sboost.Rd:27: \item in \describe must have non-empty label
checkRd: (7) sboost.Rd:28-33: \item in \describe must have non-empty label
checkRd: (7) sboost.Rd:34-35: \item in \describe must have non-empty label
checkRd: (7) sboost.Rd:36-38: \item in \describe must have non-empty label
checkRd: (7) sboost.Rd:41: \item in \describe must have non-empty label
checkRd: (7) sboost.Rd:42: \item in \describe must have non-empty label
checkRd: (7) sboost.Rd:43: \item in \describe must have non-empty label
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SBRect.Rcheck/00install.out’ for details.
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.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘spatstat.geom’

Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘httptest’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(SC2API)
  > 
  > test_check("SC2API")
  Error in library(httptest) : there is no package called 'httptest'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MMR_Distribution.Rmd’ using rmarkdown
Quitting from lines 16-24 (MMR_Distribution.Rmd) 
Error: processing vignette ‘MMR_Distribution.Rmd’ failed with diagnostics:
there is no package called 'httptest'
--- failed re-building ‘MMR_Distribution.Rmd’

SUMMARY: processing the following file failed:
  ‘MMR_Distribution.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/scagnostics.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘TAM’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘bit64’
Packages required but not available: 'R.matlab', 'gam'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/scalreg.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/scam.Rcheck/00install.out’ for details.
Packages required but not available: 'car', 'meta'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'leafem', 'leaflet', 'mapview', 'raster'
Packages required but not available:
  'neldermead', 'optimsimplex', 'optimbase'

See section ‘The DESCRIPTION file’ 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.
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggforce’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'doSNOW', 'raster', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘scDHA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'pcalg', 'Rgraphviz'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/scclust.Rcheck/00install.out’ for details.
Packages required but not available: 'ggrepel', 'irlba', 'uwot'

Package suggested but not available for checking: ‘ggrastr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory