'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'boot' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'boot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
boot_autocov: no visible global function definition for 'is.ts'
boot_autocov: no visible global function definition for 'tsboot'
boot_autocov: no visible global function definition for 'quantile'
boot_autocov: no visible global function definition for 'par'
boot_autocov: no visible global function definition for 'frequency'
boot_autocov: no visible global function definition for 'polygon'
boot_autocov: no visible global function definition for 'lines'
boot_autocov: no visible global function definition for 'abline'
boot_autocov: no visible global function definition for 'acf'
boot_spec: no visible global function definition for 'is.ts'
boot_spec: no visible global function definition for 'tsboot'
boot_spec: no visible global function definition for 'spec.pgram'
boot_spec: no visible global function definition for 'quantile'
boot_spec: no visible global function definition for 'polygon'
boot_spec: no visible global function definition for 'lines'
redraw: no visible global function definition for 'spec.pgram'
statistic: no visible global function definition for 'acf'
Undefined global functions or variables:
  abline acf frequency is.ts lines par polygon quantile spec.pgram
  tsboot
Consider adding
  importFrom("graphics", "abline", "lines", "par", "polygon")
  importFrom("stats", "acf", "frequency", "is.ts", "quantile",
             "spec.pgram")
to your NAMESPACE file.
author.search: no visible binding for global variable 'na.omit'
reference.list: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
checkRd: (7) references.list.Rd:14: \item in \value must have non-empty label
drawGraph: no visible global function definition for 'pdf'
drawGraph: no visible global function definition for 'par'
drawGraph: no visible global function definition for 'segments'
drawGraph: no visible global function definition for 'lines'
drawGraph: no visible global function definition for 'text'
drawGraph: no visible global function definition for 'dev.off'
drugRank: no visible global function definition for 'aggregate'
floating2: no visible global function definition for 'cor'
timma: no visible global function definition for 'median'
timma: no visible global function definition for 'write.table'
Undefined global functions or variables:
  aggregate cor dev.off lines median par pdf segments text write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "segments", "text")
  importFrom("stats", "aggregate", "cor", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  '_paramEst.txt'
'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
'LazyData' is specified without a 'data' directory
Found an obsolete/platform-specific call in the following function:
  '.my.tkdev'
Found the platform-specific device:
  'X11'
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
FLXmclust.Density: no visible global function definition for 'dmvnorm'
FLXmclust.Estimate: no visible global function definition for 'flexmix'
FLXmclust.Estimate: no visible global function definition for
  'FLXmclust'
coefmclust: no visible global function definition for 'parameters'
flexmix.Density: no visible global function definition for
  'model.matrix'
flexmix.Density: no visible global function definition for
  'model.response'
flexmix.Density: no visible global function definition for
  'model.frame'
flexmix.Density: no visible global function definition for 'dnorm'
flexmix.Density: no visible global function definition for 'dpois'
flexmix.Density: no visible global function definition for 'dbinom'
flexmix.Estimate: no visible global function definition for 'flexmix'
flexmix.Estimate: no visible global function definition for 'FLXglm'
tleplot,TLE-data.frame: no visible global function definition for
  'legend'
Undefined global functions or variables:
  FLXglm FLXmclust dbinom dmvnorm dnorm dpois flexmix legend
  model.frame model.matrix model.response parameters
Consider adding
  importFrom("graphics", "legend")
  importFrom("stats", "dbinom", "dnorm", "dpois", "model.frame",
             "model.matrix", "model.response")
to your NAMESPACE file.
'library' or 'require' call to 'mvtnorm' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'mvtnorm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
EMN: no visible global function definition for 'dmvnorm'
EMN: no visible global function definition for 'pmvnorm'
EMT: no visible global function definition for 'GenzBretz'
EMT: no visible global function definition for 'dmvt'
EMT: no visible global function definition for 'pmvt'
MomemNT: no visible global function definition for 'pnorm'
MomemNT: no visible global function definition for 'dnorm'
MomemNT: no visible global function definition for 'pmvnorm'
MomemNT: no visible global function definition for 'dmvnorm'
TT.moment: no visible global function definition for 'GenzBretz'
TT.moment: no visible global function definition for 'pmvt'
TT.moment: no visible global function definition for 'dt'
TT.moment: no visible global function definition for 'pt'
TT.moment: no visible global function definition for 'dmvt'
cdfNI: no visible global function definition for 'pnorm'
cdfNI: no visible global function definition for 'pt'
inits: no visible global function definition for 'lm'
Undefined global functions or variables:
  GenzBretz dmvnorm dmvt dnorm dt lm pmvnorm pmvt pnorm pt
Consider adding
  importFrom("stats", "dnorm", "dt", "lm", "pnorm", "pt")
to your NAMESPACE file.
Rd file 'UTIdata.Rd':
  \examples lines wider than 100 characters:
     x = cbind((UTIdata$Fup==0)+0, (UTIdata$Fup==1)+0, (UTIdata$Fup==3)+0, (UTIdata$Fup==6)+0, (UTIdata$Fup==9)+0, (UTIdata$Fup==12)+0, (UTI ... [TRUNCATED]

These lines will be truncated in the PDF manual.
'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
extractContentDOM: no visible global function definition for
  'capture.output'
extractHTMLStrip: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  capture.output
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
Found the following significant warnings:
  ./esf_mst_sum_vector_s2.h:54:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ./esf_mst_sum_vector_s2.h:71:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  ./esf_mst_sum_vector_s2.h:82:20: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ./esf_mst_sum_vector_s2.h:82:51: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  esf_mst_sum_vector.cpp:362:16: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  esf_mst_sum_vector.cpp:387:15: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  esf_mst_sum_vector.cpp:394:23: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  esf_mst_sum_vector.cpp:397:23: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  esf_mst_sum_vector.cpp:411:23: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  esf_mst_sum_vector.cpp:414:23: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  esf_mst_sum_vector.cpp:462:59: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/tmt.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: 'corpus.JSS.papers'
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Running examples in 'topmodel-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: topmodel
> ### Title: implementation of the hydrological model TOPMODEL
> ### Aliases: topmodel
> ### Keywords: models
> 
> ### ** Examples
> 
> data(huagrahuma)
> attach(huagrahuma)
> 
> ## returns the simulated runoff (Qobs not given)
> Qsim <- topmodel(parameters, topidx, delay, rain, ETp)
> 
> ## returns a list of simulated runoff (Q), overland flow (qo), subsurface flow (qs) and storage (S):
> Qsim <- topmodel(parameters, topidx, delay, rain,ETp, verbose = TRUE)
> 
> ## plot observed and simulated discharge:
> plot(Qobs)
> points(Qsim$Q, col="red", type="l")
> 
> ## For a Monte carlo sampling from a uniform distribution, we construct a parameter matrix:
> 
> runs<-10
> 
> qs0   <- runif(runs, min=0, max=4e-5)
> lnTe  <- runif(runs, min=-2, max=1)
> m     <- runif(runs, min=0, max=0.2)
> Sr0   <- runif(runs, min=0, max=0.02)
> Srmax <- runif(runs, min=0, max=2)
> td    <- runif(runs, min=0, max=3)
> vch   <- 1000
> vr    <- runif(runs, min=100, max=2500)
> k0    <- runif(runs, min=0, max=0.01)
> CD    <- runif(runs, min=0, max=5)
> dt    <- 0.25
> 
> parameters<-cbind(qs0,lnTe,m,Sr0,Srmax,td,vch,vr,k0,CD,dt)
> 
> ## returns an array of 10 Nash Sutcliffe efficiencies; one for each parameter set:
> result<-topmodel(parameters, topidx, delay, rain, ETp, Qobs = Qobs)
Iteration:                1       2       3       4       5       6       7       8       9      10
Error in (Qobs == -9999) && (iterations > 1) : 
  'length = 10000' in coercion to 'logical(1)'
Calls: topmodel
Execution halted
Package required but not available: 'qpgraph'

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: 'toscaData'
Malformed Description field: should contain one or more complete sentences.
Tosls.formula: no visible global function definition for 'model.matrix'
Tosls.formula: no visible global function definition for
  'model.response'
summary: no visible global function definition for 'coef'
summary: no visible global function definition for 'pt'
Undefined global functions or variables:
  coef model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
ConfA: no visible global function definition for 'qf'
EstM2Sn: no visible global function definition for 'nlm'
EstM2Sn: no visible global function definition for 'qnorm'
TV.model: no visible global function definition for 'dev.new'
TV.model: no visible global function definition for 'points'
betaBino: no visible global function definition for 'pbinom'
doseD: no visible global function definition for 'lm'
doseD: no visible global function definition for 'dev.new'
doseD: no visible global function definition for 'par'
doseD: no visible global function definition for 'axTicks'
doseD: no visible global function definition for 'axis'
doseD: no visible global function definition for 'lines'
doseD: no visible global function definition for 'abline'
doseD: no visible global function definition for 'legend'
setD: no visible global function definition for 'dev.new'
setD: no visible global function definition for 'par'
setD: no visible global function definition for 'pbinom'
setD: no visible global function definition for 'abline'
setD: no visible global function definition for 'axis'
setD: no visible global function definition for 'rect'
setD: no visible global function definition for 'lines'
setD: no visible global function definition for 'text'
setD: no visible global function definition for 'axTicks'
setD: no visible global function definition for 'legend'
spoD : spoD_A: no visible global function definition for 'chisq.test'
Undefined global functions or variables:
  abline axTicks axis chisq.test dev.new legend lines lm nlm par pbinom
  points qf qnorm rect text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axTicks", "axis", "legend", "lines",
             "par", "points", "rect", "text")
  importFrom("stats", "chisq.test", "lm", "nlm", "pbinom", "qf", "qnorm")
to your NAMESPACE file.
Found the following files/directories:
  '01_spontaneous lethality.txt' '02.sample size.txt'
  '03.dosestrategy.txt' 'doseD4.txt' 'setD.txt' 'spoDa.txt' 'spoDb.txt'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'scriptests'
Found the following calls to attach():
File 'track/R/track.attach.R':
  attach(what = NULL, pos = pos, name = name)
See section 'Good practice' in '?attach'.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running 'testthat.R' [6s/11s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(traitdataform)
  > 
  > test_check("traitdataform")
  [ FAIL 2 | WARN 0 | SKIP 4 | PASS 51 ]
  
  == Skipped tests ===============================================================
  * On CRAN (1)
  * empty test (2)
  * l10n_info()$`UTF-8` is not TRUE (1)
  
  == Failed tests ================================================================
  -- Failure (test.map_gbif_taxonomy.R:8:3): gbif taxonomy reachable -------------
  Value hashes to d37d3df9bed65e2451367aeaf98866dd, not e94508bb29c9a6b66cc2b92a92ea07f6
  -- Failure (test.map_gbif_taxonomy.R:10:3): gbif taxonomy reachable ------------
  Value hashes to 78fc839027d0fa26b64e6f856ece50b0, not d36c224f512159f3cf0b7110d0140cf9
  
  [ FAIL 2 | WARN 0 | SKIP 4 | PASS 51 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'taxidata'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'glmmsr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
microsoftTranslate: no visible global function definition for
  'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
rtrapezoid: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
checkRd: (7) Dados6.Rd:27: invalid email address: <alcineimistico@hotmail.com>
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  betaMPT.cpp:59:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  betaMPT.cpp:59:39: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  betaMPT.cpp:59:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  betaMPT.cpp:61:15: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  betaMPT.cpp:61:45: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  betaMPT.cpp:61:17: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  betaMPT.cpp:85:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  betaMPT.cpp:85:39: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  betaMPT.cpp:85:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  betaMPT.cpp:87:15: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  betaMPT.cpp:87:45: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  betaMPT.cpp:87:17: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TreeBUGS.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'TreeDistData'
'LazyData' is specified without a 'data' directory
Build_JTree: no visible global function definition for 'flush.console'
Run_JTree: no visible global function definition for 'cov2cor'
Undefined global functions or variables:
  cov2cor flush.console
Consider adding
  importFrom("stats", "cov2cor")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Installation failed.
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/treenomial.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title 'Vignette Title':
  'trimr-vignette.Rmd'
cinbag: no visible global function definition for 'var'
trimTrees: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict var
Consider adding
  importFrom("stats", "predict", "var")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'gtools' 'mgcv'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'gtools' 'mgcv' 'msm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HtoGp: no visible global function definition for 'odd'
HtoGp: no visible global function definition for 'even'
plot.pirls.gam: no visible global function definition for 'par'
plot.pirls.gam: no visible global function definition for 'title'
plot.pirls.gam: no visible global function definition for 'lines'
plot.pirls.gam: no visible global function definition for 'rug'
plot.pirls.gam: no visible global function definition for 'mtext'
test.trioGxE: no visible global function definition for 'write.table'
trioGxE: no visible global function definition for 'quantile'
trioGxE: no visible global function definition for 'qtnorm'
trioplot: no visible global function definition for 'quantile'
trioplot: no visible global function definition for 'formula'
trioplot: no visible global function definition for 'gam'
trioplot: no visible global function definition for 'binomial'
Undefined global functions or variables:
  binomial even formula gam lines mtext odd par qtnorm quantile rug
  title write.table
Consider adding
  importFrom("graphics", "lines", "mtext", "par", "rug", "title")
  importFrom("stats", "binomial", "formula", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
DrawMargin: no visible global function definition for 'qnorm'
DrawProbability: no visible global function definition for 'pnorm'
Factor: no visible global function definition for 'new'
Gaussian: no visible global function definition for 'new'
LikelihoodFactor: no visible global function definition for 'new'
Parameters: no visible global function definition for 'new'
Player: no visible global function definition for 'new'
PriorFactor: no visible global function definition for 'new'
SumFactor: no visible global function definition for 'new'
TruncateFactor: no visible global function definition for 'new'
Variable: no visible global function definition for 'new'
Vdraw: no visible global function definition for 'dnorm'
Vdraw: no visible global function definition for 'pnorm'
Vwin: no visible global function definition for 'dnorm'
Vwin: no visible global function definition for 'pnorm'
Wdraw: no visible global function definition for 'dnorm'
Wdraw: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dnorm new pnorm qnorm
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dnorm", "pnorm", "qnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'MASS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cdens: no visible global function definition for 'head'
dplot: no visible global function definition for 'knots'
dplot: no visible global function definition for 'median'
dplot: no visible global function definition for 'par'
dplot: no visible global function definition for 'plot.stepfun'
dplot: no visible global function definition for 'abline'
edf: no visible global function definition for 'approxfun'
mctest : rdist: no visible global function definition for 'runif'
mctest : S: no visible global function definition for 'optim'
qplot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline approxfun head knots median optim par plot.stepfun runif
Consider adding
  importFrom("graphics", "abline", "par")
  importFrom("stats", "approxfun", "knots", "median", "optim",
             "plot.stepfun", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (7) arima.Rd:37-40: \item in \arguments must have non-empty label
checkRd: (7) arimax.Rd:36-39: \item in \arguments must have non-empty label
tfDetails: no visible global function definition for 'start'
tfDetails: no visible global function definition for 'end'
Undefined global functions or variables:
  end start
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
Qhat: no visible global function definition for 'pnorm'
plrt: no visible global function definition for 'uniroot'
plrt: no visible global function definition for 'optimize'
simulatedata: no visible global function definition for 'rnorm'
tsc.test: no visible global function definition for 'shapiro.test'
tsc.test: no visible global function definition for 'p.adjust'
tsc.test: no visible global function definition for 'glm'
tsc.test : f: no visible global function definition for 'pnorm'
tsc.test: no visible global function definition for 'uniroot'
tsc.test: no visible global function definition for 'optimize'
variance: no visible global function definition for 'density'
variance: no visible global function definition for 'ecdf'
Undefined global functions or variables:
  density ecdf glm optimize p.adjust pnorm rnorm shapiro.test uniroot
Consider adding
  importFrom("stats", "density", "ecdf", "glm", "optimize", "p.adjust",
             "pnorm", "rnorm", "shapiro.test", "uniroot")
to your NAMESPACE file.
'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
Running examples in 'tseries-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get.hist.quote
> ### Title: Download Historical Finance Data
> ### Aliases: get.hist.quote
> ### Keywords: ts
> 
> ### ** Examples
> 
> con <- url("https://finance.yahoo.com")
> if(!inherits(try(open(con), silent = TRUE), "try-error")) {
+   close(con)
+   x <- get.hist.quote(instrument = "^gspc", start = "1998-01-01",
+                       quote = "Close")
+   plot(x)
+ 
+   x <- get.hist.quote(instrument = "ibm", quote = c("Cl", "Vol"))
+   plot(x, main = "International Business Machines Corp")
+ 
+   spc <- get.hist.quote(instrument = "^gspc", start = "1998-01-01",
+          quote = "Close")
+   ibm <- get.hist.quote(instrument = "ibm",  start = "1998-01-01",
+          quote = "Adj")
+   require("zoo")		# For merge() method.
+   x <- merge(spc, ibm)
+   plot(x, main = "IBM vs S&P 500")
+ }
'getSymbols' currently uses auto.assign=TRUE by default, but will
use auto.assign=FALSE in 0.5-0. You will still be able to use
'loadSymbols' to automatically load data. getOption("getSymbols.env")
and getOption("getSymbols.auto.assign") will still be checked for
alternate defaults.

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

Error in new.session() : Could not establish session after 5 attempts.
Calls: get.hist.quote ... do.call -> getSymbols.yahoo -> .getHandle -> new.session
Execution halted
vintageMap: no visible global function definition for 'read.table'
TSget,character-TSfameLocalConnection: no visible global function
  definition for 'as.ts'
TSget,character-TSfameLocalConnection: no visible global function
  definition for 'zoo'
TSget,character-TSfameLocalConnection: no visible global function
  definition for 'frequency'
TSget,character-TSfameServerConnection: no visible global function
  definition for 'as.ts'
TSget,character-TSfameServerConnection: no visible global function
  definition for 'zoo'
TSget,character-TSfameServerConnection: no visible global function
  definition for 'frequency'
Undefined global functions or variables:
  as.ts frequency read.table zoo
Consider adding
  importFrom("stats", "as.ts", "frequency")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Func.SAX: no visible global function definition for 'sd'
Func.SAX: no visible global function definition for 'qnorm'
Func.matrix: no visible global function definition for 'qnorm'
Func.motif: no visible global function definition for 'sd'
Func.motif: no visible global function definition for 'na.omit'
Func.motif: no visible global function definition for 'combn'
Func.motif.multivariate: no visible global function definition for
  'txtProgressBar'
Func.motif.multivariate: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  combn na.omit qnorm sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "qnorm", "sd")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
dLag : dlag.f: no visible global function definition for
  'complete.cases'
distmat: no visible global function definition for 'dist'
fitCity: no visible global function definition for 'glm.control'
fitCity: no visible global function definition for 'terms'
ldmvnorm: no visible global function definition for 'mahalanobis'
lspline: no visible global function definition for 'quantile'
plot.tsdecomp: no visible global function definition for 'par'
setupFormula: no visible global function definition for 'as.formula'
spatialgibbs: no visible global function definition for 'rnorm'
spatialgibbs: no visible global function definition for 'rgamma'
spatialgibbs: no visible global function definition for 'runif'
tsdecomp: no visible global function definition for 'fft'
Undefined global functions or variables:
  as.formula complete.cases dist fft glm.control mahalanobis par
  quantile rgamma rnorm runif terms
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "as.formula", "complete.cases", "dist", "fft",
             "glm.control", "mahalanobis", "quantile", "rgamma", "rnorm",
             "runif", "terms")
to your NAMESPACE file.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
.help.ESS: no visible global function definition for 'index.search'
TransSphere : ttin: no visible global function definition for 't.test'
TransSphere: no visible global function definition for 'sd'
TransSphere: no visible global function definition for 'quantile'
TransSphere: no visible global function definition for 'pt'
Undefined global functions or variables:
  index.search pt quantile sd t.test
Consider adding
  importFrom("stats", "pt", "quantile", "sd", "t.test")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'TSTr.Rmd' using rmarkdown
Quitting from lines 167-170 (TSTr.Rmd) 
Error: processing vignette 'TSTr.Rmd' failed with diagnostics:
'length = 1197' in coercion to 'logical(1)'
--- failed re-building 'TSTr.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  'XMIwords.txt'
TT.GS : TT.GS.sp: no visible global function definition for 'qt'
TT.GS : TT.GS.sp: no visible global function definition for 'runif'
TT.GS : TT.GS.sp: no visible global function definition for 'pt'
TT.moment: no visible global function definition for 'dt'
TT.moment: no visible global function definition for 'pt'
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
ttwa: no visible global function definition for 'aggregate'
ttwa: no visible global function definition for 'txtProgressBar'
ttwa: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  aggregate setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (7) post.Rd:21: \item in \arguments must have non-empty label
checkRd: (7) post.edit.Rd:22: \item in \arguments must have non-empty label
checkRd: (7) post.reblog.Rd:21: \item in \arguments must have non-empty label
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package in Depends field not imported from: 'tcltk'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
TwoCop: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'sl3'
'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
Crm: no visible global function definition for 'integrate'
Crm : <anonymous>: no visible global function definition for
  'integrate'
Crm: no visible global function definition for 'optimize'
ail1: no visible global function definition for 'uniroot'
ail2 : fu : <anonymous>: no visible global function definition for
  'integrate'
ail2: no visible global function definition for 'uniroot'
aip : fu : <anonymous>: no visible global function definition for
  'integrate'
aip: no visible global function definition for 'uniroot'
ait1: no visible global function definition for 'uniroot'
ait2 : fu : <anonymous>: no visible global function definition for
  'integrate'
ait2: no visible global function definition for 'uniroot'
sim3p3: no visible global function definition for 'rbinom'
simCrm: no visible global function definition for 'rbinom'
simCrm: no visible global function definition for 'palette'
simCrm: no visible global function definition for 'gray'
simCrm: no visible global function definition for 'abline'
simCrm: no visible global function definition for 'lines'
ssim3p3: no visible global function definition for 'txtProgressBar'
ssim3p3: no visible global function definition for 'setTxtProgressBar'
ssimCrm: no visible global function definition for 'txtProgressBar'
ssimCrm: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  abline gray integrate lines optimize palette rbinom setTxtProgressBar
  txtProgressBar uniroot
Consider adding
  importFrom("grDevices", "gray", "palette")
  importFrom("graphics", "abline", "lines")
  importFrom("stats", "integrate", "optimize", "rbinom", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Found the following significant warnings:
  simz.cpp:31:14: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ubms.Rcheck/00install.out' for details.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
rmd2pdf: no visible global function definition for 'tail'
rnw2pdf: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'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
ubRacing : predCandidate: no visible global function definition for
  'predict'
ubRacing : aux2.friedman.edit: no visible global function definition
  for 'pchisq'
ubRacing : aux2.friedman.edit: no visible global function definition
  for 'qt'
ubRacing : aux.friedman.edit: no visible global function definition for
  'wilcox.test'
ubRacing : aux.ttest.edit: no visible global function definition for
  't.test'
ubRacing : aux.ttest.edit: no visible global function definition for
  'p.adjust'
ubRacing : idFolds: no visible global function definition for
  'quantile'
ubRacing: no visible binding for global variable 'sd'
ubSmoteExs: no visible global function definition for 'runif'
Undefined global functions or variables:
  p.adjust pchisq predict qt quantile runif sd t.test wilcox.test
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "predict", "qt", "quantile",
             "runif", "sd", "t.test", "wilcox.test")
to your NAMESPACE file.
'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
dudewicz.unif.test: no visible global function definition for 'runif'
frosini.unif.test: no visible global function definition for 'runif'
hegazy.unif.test: no visible global function definition for 'runif'
kolmogorov.unif.test: no visible global function definition for 'runif'
kuiper.unif.test: no visible global function definition for 'runif'
neyman.unif.test: no visible global function definition for 'runif'
quesenberry.unif.test: no visible global function definition for
  'runif'
sarkadi.unif.test: no visible global function definition for 'runif'
sherman.unif.test: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
cumcount: no visible global function definition for 'setNames'
uniqtag: no visible global function definition for 'setNames'
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'VariantAnnotation'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'Tutorial.Rmd' using rmarkdown
Quitting from lines 110-111 (Tutorial.Rmd) 
Error: processing vignette 'Tutorial.Rmd' failed with diagnostics:
lexical error: invalid char in json text.
                                       <!DOCTYPE HTML> <html lang="en-
                     (right here) ------^

--- failed re-building 'Tutorial.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'USAboundariesData'
Package suggested but not available for checking: 'USA.state.boundaries.data'
Package suggested but not available for checking: 'diseasemapping'
readSEER: no visible global function definition for 'read.fwf'
Undefined global functions or variables:
  read.fwf
Consider adding
  importFrom("utils", "read.fwf")
to your NAMESPACE file.
Unknown package 'diseasemapping' in Rd xrefs
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'UScensus2000cdp/R/zzz.R':
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000cdp\").\n")
    cat("Type help(package=\"UScensus2000cdp\") to get started.\n")

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

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ensembldb', 'GenomicFeatures'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
histw: no visible global function definition for 'plot.new'
histw: no visible global function definition for 'plot.window'
histw: no visible global function definition for 'axis'
histw: no visible global function definition for 'rect'
histw: no visible global function definition for 'lines'
uwham.boot: no visible binding for global variable 'var'
Undefined global functions or variables:
  axis lines plot.new plot.window rect var
Consider adding
  importFrom("graphics", "axis", "lines", "plot.new", "plot.window",
             "rect")
  importFrom("stats", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'PredValidationPlots.pdf' 'RepStructValidationPlots.pdf'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ../inst/include/gdalgeometry/gdalgeometry.h:230:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ../inst/include/gdalgeometry/gdalgeometry.h:241:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ../inst/include/gdalgeometry/gdalgeometry.h:291:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ../inst/include/gdalgeometry/gdalgeometry.h:302:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ../inst/include/gdalgeometry/gdalgeometry.h:354:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ../inst/include/gdalgeometry/gdalgeometry.h:365:11: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ../inst/include/gdalgeometry/gdalgeometry.h:421:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  ../inst/include/gdalgeometry/gdalgeometry.h:432:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/vapour.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
Package vignette with placeholder title 'Vignette Title':
  'intro-to-varbundle.Rmd'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Mammen: no visible global function definition for 'runif'
PR2: no visible global function definition for 'ar.burg'
PR2: no visible global function definition for 'pt'
PR2: no visible global function definition for 'pf'
PR3: no visible global function definition for 'ar.burg'
PR3: no visible global function definition for 'pt'
PR3: no visible global function definition for 'pf'
VAR.FOR: no visible global function definition for 'qnorm'
VAR.ForeB: no visible global function definition for 'runif'
VAR.LRtest: no visible global function definition for 'pchisq'
VAR.LRtest: no visible global function definition for 'pf'
VAR.PI: no visible global function definition for 'quantile'
VAR.Waldtest: no visible global function definition for 'pf'
VAR.irf: no visible global function definition for 'par'
VAR.irf: no visible global function definition for 'abline'
VAR1.sim: no visible global function definition for 'rnorm'
resamp: no visible global function definition for 'runif'
Undefined global functions or variables:
  abline ar.burg par pchisq pf pt qnorm quantile rnorm runif
Consider adding
  importFrom("graphics", "abline", "par")
  importFrom("stats", "ar.burg", "pchisq", "pf", "pt", "qnorm",
             "quantile", "rnorm", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
black_scholes: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
burdenPlot: no visible global function definition for 'density'
burdenPlot: no visible global function definition for 'axis'
burdenPlot: no visible global function definition for 'points'
burdenPlot: no visible global function definition for 'lines'
burdenPlot: no visible global function definition for 'abline'
burdenPlot: no visible global function definition for 'text'
burdenPlot: no visible global function definition for 'sd'
burdenPlot: no visible global function definition for 'segments'
vbdm: no visible global function definition for 'var'
vbdm: no visible global function definition for 'pchisq'
vbdmR : run_discrete_mixture_vanilla: no visible global function
  definition for 'var'
vbdmR: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  abline axis density lines pchisq points sd segments text var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "points", "segments",
             "text")
  importFrom("stats", "density", "pchisq", "sd", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
compute_KL : rtnorm: no visible global function definition for 'runif'
compute_KL : rtnorm: no visible global function definition for 'dnorm'
compute_KL: no visible global function definition for 'qnorm'
compute_KL: no visible global function definition for 'dnorm'
compute_KL: no visible global function definition for 'pnorm'
compute_KL: no visible global function definition for 'var'
compute_KL: no visible global function definition for 'rbinom'
compute_KL: no visible global function definition for 'rnorm'
compute_KL: no visible global function definition for 'sd'
vbsr: no visible global function definition for 'qchisq'
vbsr: no visible global function definition for 'var'
vbsr: no visible global function definition for 'pchisq'
vbsr: no visible global function definition for 'sd'
vbsr: no visible binding for global variable 'sd'
Undefined global functions or variables:
  dnorm pchisq pnorm qchisq qnorm rbinom rnorm runif sd var
Consider adding
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qchisq", "qnorm",
             "rbinom", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Package vignette with placeholder title 'Vignette Title':
  'VBTree_vignette.Rmd'
Found the following significant warnings:
  NM2winNM.cpp:145:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  extract_gt.cpp:362:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  freq_peak.cpp:400:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  freq_peak.cpp:405:13: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  read_vcfR.cpp:497:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  vcfRCommon.cpp:112:9: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/vcfR.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Compare2FDS: no visible global function definition for 'runif'
Compare2FDS: no visible global function definition for 'lm'
Compare2FDS: no visible global function definition for 'model.matrix'
Compare2FDS: no visible global function definition for 'abline'
Compare2FDS: no visible global function definition for 'lines'
Compare2FDS: no visible global function definition for 'text'
Compare2Vdg: no visible global function definition for 'par'
Compare2Vdg: no visible global function definition for 'lines'
Compare2Vdg: no visible global function definition for 'legend'
FDSPlot: no visible global function definition for 'runif'
FDSPlot: no visible global function definition for 'lm'
FDSPlot: no visible global function definition for 'model.matrix'
FDSPlot: no visible global function definition for 'abline'
Vdgraph: no visible global function definition for 'par'
Vdgraph: no visible global function definition for 'lines'
Vdgraph: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline legend lines lm model.matrix par runif text
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "text")
  importFrom("stats", "lm", "model.matrix", "runif")
to your NAMESPACE file.
DrawDensity3D: no visible global function definition for 'colorRamp'
DrawDensity3D: no visible global function definition for 'rgb'
ReadFromFile3D: no visible global function definition for 'read.table'
Undefined global functions or variables:
  colorRamp read.table rgb
Consider adding
  importFrom("grDevices", "colorRamp", "rgb")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  vliC.cpp:539:7: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/VeryLargeIntegers.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
Malformed Title field: should not end in a period.
vif: no visible global function definition for 'sd'
vif: no visible global function definition for 'lm'
vif: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  lm pnorm sd
Consider adding
  importFrom("stats", "lm", "pnorm", "sd")
to your NAMESPACE file.
Rd file 'vif.Rd':
  \usage lines wider than 90 characters:
             vif(y, x, w0 = 0.05, dw = 0.05, subsize = 200, trace = TRUE, mode = c("dense", "sparse"))
  \examples lines wider than 100 characters:
             vif.sel <- vif(housingexp$y, housingexp$x, w0 = 0.0005, dw = 0.005, subsize = 300, trace = FALSE);

These lines will be truncated in the PDF manual.
'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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Decile.Plot: no visible global function definition for 'barplot'
Decile.Plot: no visible global function definition for 'axis'
Sliding.Window: no visible global function definition for 'lines'
Sliding.Window: no visible global function definition for 'legend'
Undefined global functions or variables:
  axis barplot legend lines
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Running examples in 'voluModel-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: smoothRaster
> ### Title: Smooth rasters
> ### Aliases: smoothRaster
> ### Keywords: dataPrep
> 
> ### ** Examples
> 
> library(raster)
Loading required package: sp
> library(fields)
Loading required package: spam
Spam version 2.8-0 (2022-01-05) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

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

    backsolve, forwardsolve

Loading required package: viridis
Loading required package: viridisLite

Try help(fields) to get started.
> # Create sample raster
> r <- raster(ncol=100, nrow=100)
> values(r) <- 1:10000
> 
> # Introduce a "bubble"
> values(r)[520:525] <- 9999
> plot(r)
> 
> # Smooth bubble with smoothRaster
> smoothedRaster <- smoothRaster(r)
Warning: 
Grid searches over lambda (nugget and sill variances) with  minima at the endpoints: 
  (GCV) Generalized Cross-Validation 
   minimum at  right endpoint  lambda  =  3.025469e-06 (eff. df= 593.75 )
> plot(smoothedRaster)
> 
> fastSmooth <- smoothRaster(r, fast = TRUE, aRange = 3.0)
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'diag': Lapack routine dgesv: system is exactly singular: U[1,1] = 0
Calls: smoothRaster ... solve -> solve -> solve.default -> .handleSimpleError -> h
Execution halted
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
voss1d: no visible global function definition for 'approx'
voss1d: no visible global function definition for 'rnorm'
voss1g: no visible global function definition for 'dchisq'
voss1g: no visible global function definition for 'approx'
voss1g: no visible global function definition for 'rnorm'
voss2d: no visible global function definition for 'rnorm'
voss2g: no visible global function definition for 'dchisq'
voss2g: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  approx dchisq rnorm
Consider adding
  importFrom("stats", "approx", "dchisq", "rnorm")
to your NAMESPACE file.
'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
'library' or 'require' call to 'misc3d' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Malformed Description field: should contain one or more complete sentences.
plot.vscc: no visible global function definition for 'rainbow'
plot.vscc: no visible global function definition for 'pairs'
Undefined global functions or variables:
  pairs rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "pairs")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'Calculate_WACC_in_R.Rmd' using rmarkdown
Quitting from lines 30-36 (Calculate_WACC_in_R.Rmd) 
Error: processing vignette 'Calculate_WACC_in_R.Rmd' failed with diagnostics:
server certificate verification failed. CAfile: none CRLfile: none
--- failed re-building 'Calculate_WACC_in_R.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
summary.whc: no visible global function definition for 'printCoefmat'
wahc.fit: no visible global function definition for 'pt'
wahc.fit: no visible global function definition for 'cor'
whc: no visible global function definition for 'model.frame'
whc: no visible global function definition for 'model.matrix'
whc: no visible global function definition for 'model.response'
Undefined global functions or variables:
  cor model.frame model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "printCoefmat", "pt")
to your NAMESPACE file.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'linout.csv' 'linout.pdf' 'out.csv' 'out.pdf' 'tabel_out.csv'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'ReconstructedData.txt' 'ReconstructedDataStDev.txt'
  'ResampledReconstructions.txt'
  'ResampledReconstructionsStandardVariation.txt'
Package suggested but not available for checking: 'ggvoronoi'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building 'introduction.Rmd' using rmarkdown
Quitting from lines 96-124 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'ggvoronoi'
--- failed re-building 'introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
onesamplemeantest: no visible global function definition for 'pnorm'
twosamplemeantest: no visible global function definition for 'pnorm'
wcq: no visible global function definition for 'var'
wcq: no visible global function definition for 'pnorm'
wcq.fdrc: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  p.adjust pnorm var
Consider adding
  importFrom("stats", "p.adjust", "pnorm", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'prepr'
checkRd: (7) ggele.Rd:19: \item in \value must have non-empty label
checkRd: (7) ggele.Rd:20: \item in \value must have non-empty label
checkRd: (7) ggele.Rd:21: \item in \value must have non-empty label
'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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title 'Vignette Title':
  'weco-vignette.Rmd'
'LazyData' is specified without a 'data' directory
Weighted.Box.test: no visible global function definition for 'acf'
Weighted.Box.test: no visible binding for global variable 'na.pass'
Weighted.Box.test: no visible global function definition for 'pgamma'
Weighted.Box.test: no visible global function definition for 'pchisq'
Weighted.LM.test: no visible global function definition for 'acf'
Weighted.LM.test: no visible binding for global variable 'na.pass'
Weighted.LM.test: no visible global function definition for 'pgamma'
Undefined global functions or variables:
  acf na.pass pchisq pgamma
Consider adding
  importFrom("stats", "acf", "na.pass", "pchisq", "pgamma")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Bundesliga.Mannschaft: no visible global function definition for 'data'
Bundesliga.Mannschaft: no visible binding for global variable
  'Bundesliga'
Bundesliga.Tabelle: no visible global function definition for 'data'
Bundesliga.Tabelle: no visible binding for global variable 'Bundesliga'
Bundesliga.XML: no visible global function definition for 'data'
Bundesliga.XML: no visible binding for global variable 'Bundesliga'
sens.spec: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File 'wikibooks/R/Bundesliga.Mannschaft.R':
  data(Bundesliga)
File 'wikibooks/R/Bundesliga.Tabelle.R':
  data(Bundesliga)
File 'wikibooks/R/Bundesliga.XML.R':
  data(Bundesliga)
See section 'Good practice' in '?data'.
Found the following files/directories:
  'Bundesliga.xml' 'myfile.xml'
'LazyData' is specified without a 'data' directory
wilcox.selection.split: no visible global function definition for
  'pnorm'
wilcox.test2: no visible global function definition for 'wilcox.test'
Undefined global functions or variables:
  pnorm wilcox.test
Consider adding
  importFrom("stats", "pnorm", "wilcox.test")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title 'Vignette Title':
  'WindCurves_Info.Rmd'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
dbayes: no visible global function definition for 'mahalanobis'
dbayes: no visible global function definition for 'var'
wmd: no visible global function definition for 'cor'
wmd: no visible global function definition for 'var'
Undefined global functions or variables:
  cor mahalanobis var
Consider adding
  importFrom("stats", "cor", "mahalanobis", "var")
to your NAMESPACE file.
fit,Leader: no visible global function definition for 'lm'
plotfit,Leader: no visible global function definition for 'par'
Undefined global functions or variables:
  lm par
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "lm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  'plyr' 'reshape2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
wordmatch: no visible global function definition for 'llply'
wordmatch : <anonymous>: no visible global function definition for
  'llply'
wordmatch: no visible global function definition for 'melt'
wordmatch: no visible global function definition for 'count'
Undefined global functions or variables:
  count llply melt
Found the following files/directories:
  'aphiainfo.csv' 'tax.csv'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (7) wowa.Rd:14: \item in \value must have non-empty label
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title 'Vignette Title':
  'wTOvignette.Rmd'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (7) crossVal-methods.Rd:90: \item in \value must have non-empty label
checkRd: (7) x12-methods.Rd:38: \item in \describe must have non-empty label
checkRd: (7) x12-methods.Rd:39: \item in \describe must have non-empty label
checkRd: (7) x12-methods.Rd:40: \item in \describe must have non-empty label
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'RP2_data_1.txt' 'RP2_data_4.txt' 'RP2_qtl_1.txt' 'RP2_qtl_4.txt'
  'hp1_effect_qtl.txt' 'hp1_freq_mrk.txt' 'hp1_freq_qtl.txt'
  'hp1_genome.txt' 'hp1_last_hp_data.txt' 'hp1_lm_mrk.txt'
  'hp1_lm_qtl.txt' 'hp1_lm_qtl_mrk.txt' 'hp1_mrk.txt' 'hp1_qtl.txt'
  'hp2_effect_qtl.txt' 'hp2_freq_mrk.txt' 'hp2_freq_qtl.txt'
  'hp2_genome.txt' 'hp2_last_hp_data.txt' 'hp2_lm_mrk.txt'
  'hp2_lm_qtl.txt' 'hp2_lm_qtl_mrk.txt' 'hp2_mrk.txt' 'hp2_qtl.txt'
  'my_RP_data_1.txt' 'my_RP_data_4.txt' 'my_RP_mrk_1.txt'
  'my_RP_mrk_4.txt'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'xgb.txt'
GNU make is a SystemRequirements.
XHWE: no visible global function definition for 'read.table'
result: no visible global function definition for 'pchisq'
result: no visible global function definition for 'rbinom'
result: no visible global function definition for 'rmultinom'
Undefined global functions or variables:
  pchisq rbinom read.table rmultinom
Consider adding
  importFrom("stats", "pchisq", "rbinom", "rmultinom")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  'results.txt'
'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
R5.value.default: no visible binding for global variable 'data.table'
R5.value.default: no visible global function definition for
  'as.data.table'
R5.value.parse: no visible binding for global variable 'data.table'
R5.value.parse: no visible global function definition for
  'is.data.table'
R5.value.parse: no visible global function definition for
  'as.data.table'
stampme: no visible global function definition for 'flush.console'
stampmsg: no visible global function definition for 'flush.console'
write.data.table: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  as.data.table data.table flush.console is.data.table write.table
Consider adding
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (7) npc.coverage.Rd:55-56: \item in \describe must have non-empty label
checkRd: (7) npc.coverage.Rd:68-70: \item in \describe must have non-empty label
checkRd: (7) npc.coverage.Rd:76-77: \item in \describe must have non-empty label
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  'xtable.html' 'xtable.tex'
Found the following files/directories:
  'OPT.csv' 'testTecan_defaultLiquid.csv' 'testTecan_setLiquid.csv'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title 'Vignette Title':
  'vignette.Rmd'
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
big.read.table: no visible global function definition for 'read.table'
big.read.table: no visible global function definition for 'object.size'
sparkline: no visible global function definition for 'is.ts'
sparkline: no visible global function definition for 'time'
sparkline: no visible global function definition for 'boxplot'
Undefined global functions or variables:
  boxplot is.ts object.size read.table time
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "is.ts", "time")
  importFrom("utils", "object.size", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  'CO2.csv'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
.NS.estimator: no visible global function definition for 'lm'
.NS.estimator: no visible global function definition for 'coef'
.NS.estimator: no visible global function definition for 'na.omit'
.NS.estimator: no visible global function definition for 'resid'
.NSS.estimator: no visible global function definition for 'lm'
.NSS.estimator: no visible global function definition for 'coef'
.NSS.estimator: no visible global function definition for 'na.omit'
.NSS.estimator: no visible global function definition for 'resid'
NSrates: no visible global function definition for 'time'
Nelson.Siegel: no visible global function definition for 'optimize'
Srates: no visible global function definition for 'time'
Svensson: no visible global function definition for 'median'
Svensson: no visible global function definition for 'optimize'
Undefined global functions or variables:
  coef lm median na.omit optimize resid time
Consider adding
  importFrom("stats", "coef", "lm", "median", "na.omit", "optimize",
             "resid", "time")
to your NAMESPACE file.
Rd file 'ECBYieldCurve.Rd':
  \examples lines wider than 100 characters:
     plot(mat.ECB, ECBYieldCurve[i,], type="o", xlab="Maturities structure in years", ylab="Interest rates values")

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

These lines will be truncated in the PDF manual.
kmeansN: no visible global function definition for 'kmeans'
kmeansN: no visible global function definition for 'aggregate'
kmeansN2: no visible global function definition for 'aggregate'
kmeansN2: no visible binding for global variable 'sd'
Undefined global functions or variables:
  aggregate kmeans sd
Consider adding
  importFrom("stats", "aggregate", "kmeans", "sd")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package required but not available: 'ghyp'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  ae.cpp:8:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/yuima.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'RNRCS'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  rcpparma_hello_world.cpp:377:37: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ziphsmm.Rcheck/00install.out' for details.
Package vignette with placeholder title 'Vignette Title':
  'ZipRadius.Rmd'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'zdat'
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: 'SDMTools'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  fnToExport.cpp:415:8: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See '/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ZVCV.Rcheck/00install.out' for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/A3.Rcheck/00install.out’ for details.
Packages required but not available:
  'Bios2cor', 'seqinr', 'plotly', 'Hmisc'

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 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/ABCp2.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: 'readr', 'doParallel'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘vegan’
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(abdiv)
  > 
  > test_check("abdiv")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 566 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-alpha.R:64:3): Alpha diversity values are consistent with vegan ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'vegan'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(richness(bci19), vegan::specnumber(bci19)) at test-alpha.R:64:2
   2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
   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)
  ── Error (test-beta.R:25:3): Distance functions are consistent with vegan::vegdist() ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'vegan'
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-beta.R:25:2
   2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─abdiv from_vegdist(x1, x2, "manhattan")
   5. └─base::loadNamespace(x) at test-beta.R:23:4
   6.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   7.     └─base withOneRestart(expr, restarts[[1L]])
   8.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 566 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘mosaic’

Packages suggested but not available for checking:
  'car', 'HH', 'vcd', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
multiplot: no visible global function definition for ‘rainbow’
multiplot: no visible global function definition for ‘text’
multiplot: no visible global function definition for ‘lines’
multiplot: no visible global function definition for ‘par’
plot.abf2: no visible global function definition for ‘abline’
plot.abf2: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline lines par rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "par", "text")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'rjags', 'lme4', 'graph', 'Rgraphviz', 'doParallel'

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

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/abodOutlier.Rcheck/00install.out’ for details.
Package required but not available: ‘emojifont’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'tmap', 'pct'
Error(s) in re-building vignettes:
  ...
--- re-building ‘abstr.Rmd’ using rmarkdown
Quitting from lines 40-45 (abstr.Rmd) 
Error: processing vignette ‘abstr.Rmd’ failed with diagnostics:
there is no package called 'tmap'
--- failed re-building ‘abstr.Rmd’

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/abundant.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Ac3net.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'devtools', 'httptest'
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(academictwitteR)
  > 
  > test_check("academictwitteR")
  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 ‘academictwitteR-auth.Rmd’ using rmarkdown
--- finished re-building ‘academictwitteR-auth.Rmd’

--- re-building ‘academictwitteR-batchcompliance.Rmd’ using rmarkdown
--- finished re-building ‘academictwitteR-batchcompliance.Rmd’

--- re-building ‘academictwitteR-build.Rmd’ using rmarkdown
Quitting from lines 33-35 (academictwitteR-build.Rmd) 
Error: processing vignette ‘academictwitteR-build.Rmd’ failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘academictwitteR-build.Rmd’

--- re-building ‘academictwitteR-errors.Rmd’ using rmarkdown
--- finished re-building ‘academictwitteR-errors.Rmd’

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

--- re-building ‘academictwitteR-tidy.Rmd’ using rmarkdown
--- finished re-building ‘academictwitteR-tidy.Rmd’

SUMMARY: processing the following file failed:
  ‘academictwitteR-build.Rmd’

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

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

Package suggested but not available for checking: ‘plotly’

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

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

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/ACDC.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
print.funlinWLS: no visible global function definition for ‘pchisq’
print.linML: no visible global function definition for ‘pchisq’
print.loglinML: no visible global function definition for ‘pchisq’
print.satMarML: no visible global function definition for ‘pchisq’
print.satMcarWLS: no visible global function definition for ‘pchisq’
summary.funlinWLS: no visible global function definition for ‘pchisq’
summary.linML: no visible global function definition for ‘pchisq’
summary.loglinML: no visible global function definition for ‘pchisq’
summary.satMarML: no visible global function definition for ‘pchisq’
summary.satMcarWLS: no visible global function definition for ‘pchisq’
summary.waldTest: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘randtoolbox’

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/acfMPeriod.Rcheck/00install.out’ for details.
Packages required but not available: 'gamlss', 'gamlss.dist', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'aroma.affymetrix', 'R.oo', 'R.utils', 'R.filesets', 'aroma.core'

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

--- re-building ‘autocorrelation.Rmd’ using rmarkdown
Quitting from lines 21-23 (autocorrelation.Rmd) 
Error: processing vignette ‘autocorrelation.Rmd’ failed with diagnostics:
there is no package called 'R.utils'
--- failed re-building ‘autocorrelation.Rmd’

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘cosinor2’

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

Packages suggested but not available for checking:
  'raster', 'gdistance', 'rgdal', 'RGtk2', 'gWidgets2RGtk2',
  'gWidgets2'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'BSgenome', 'BSgenome.Hsapiens.UCSC.hg19',
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm9',
  'BSgenome.Mmusculus.UCSC.mm10', 'Biostrings', 'GenomeInfoDb',
  'GenomicRanges', 'IRanges', 'S4Vectors'

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: ‘insol’

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.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘imager’

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: 'caret', 'doParallel'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
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/AdaptFitOS.Rcheck/00install.out’ for details.
Package required but not available: ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/adaptMCMC.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘glmnet’
Error(s) in re-building vignettes:
  ...
--- re-building ‘adapt_demo.Rmd’ using rmarkdown
Quitting from lines 212-213 (adapt_demo.Rmd) 
Error: processing vignette ‘adapt_demo.Rmd’ failed with diagnostics:
'glmnet' package is required for 'adapt_glmnet'. Please intall.
--- failed re-building ‘adapt_demo.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'missForest', 'ComICS', 'doParallel', 'quantmod', 'pcaMethods'

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

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/ada.Rcheck/00install.out’ for details.
Package required but not available: ‘caret’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/addhaz.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
Package required but not available: ‘Benchmarking’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'recipes'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/additive.Rcheck/00install.out’ for details.
critical.values: no visible global function definition for ‘rnorm’
critical.values: no visible global function definition for ‘quantile’
mandel.test: no visible global function definition for ‘qf’
mtukey.test : p.test: no visible global function definition for ‘qf’
mtukey.test: no visible binding for global variable ‘quantile’
mtukey.test: no visible global function definition for ‘rnorm’
tukey.test: no visible global function definition for ‘qf’
Undefined global functions or variables:
  qf quantile rnorm
Consider adding
  importFrom("stats", "qf", "quantile", "rnorm")
to your NAMESPACE file.
Package required but not available: ‘turboEM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/addScales.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ADDT.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'ade4TkGUI', 'adegraphics', 'adephylo', 'CircStats', 'spdep',
  'splancs', 'doParallel'
Package required but not available: ‘adegraphics’

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

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

Packages suggested but not available for checking:
  'adespatial', 'pegas', 'hierfstat', 'spdep', 'splancs', 'poppr'

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

Packages suggested but not available for checking:
  'maptools', 'spdep', 'splancs'

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

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: 'adehabitatMA', 'adehabitatHR'

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: 'adehabitatMA', 'CircStats'

Package suggested but not available for checking: ‘maptools’

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ProTrackR’
Malformed Description field: should contain one or more complete sentences.
Skipping vignette re-building
Packages suggested but not available for checking: 'R.rsp', 'AdhereRViz'

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

... incomplete output.  Crash?
when running code in ‘calling-AdhereR-from-python3.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘AdhereR-overview.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘calling-AdhereR-from-python3.Rmd’ using ‘UTF-8’... failed to complete the test
Packages required but not available: 'RMariaDB', 'RSQLite'

Packages suggested but not available for checking:
  'readODS', 'haven', '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:
  'adegraphics', 'adephylo', 'FactoMineR', 'phylobase', 'phytools'

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

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

Packages suggested but not available for checking:
  'rioja', 'HiTC', 'snpStats'

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: ‘EbayesThresh’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ADMMnet.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: ‘doParallel’

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

Package suggested but not available for checking: ‘shinystan’

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.
Package required but not available: ‘fields’

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: ‘spatstat.geom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/AdvBinomApps.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Running examples in ‘advclust-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: biploting
> ### Title: Biploting Fuzzy Cluster Result
> ### Aliases: biploting
> 
> ### ** Examples
> 
> fuzzy.CM(iris[,1:4],K=3,m=2,max.iteration=100,threshold=1e-5,RandomNumber=1234)->cl1

Membership initialiazed randomly
Error in member(object) < 0 || member(object) > 1 : 
  'length = 450' in coercion to 'logical(1)'
Calls: fuzzy.CM ... validObject -> anyStrings -> isTRUE -> validityMethod
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘advclust.Rmd’ using rmarkdown
Quitting from lines 28-32 (advclust.Rmd) 
Error: processing vignette ‘advclust.Rmd’ failed with diagnostics:
'length = 450' in coercion to 'logical(1)'
--- failed re-building ‘advclust.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'BayesFactor', 'car', 'effects', 'GGally', 'Hmisc', 'readr',
  'robust', 'sjstats', 'WRS2'

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

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: ‘doParallel’

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: 'car', 'lmtest'

Packages suggested but not available for checking:
  'dynlm', 'effects', 'fGarch', 'forecast', 'mlogit', 'np', 'plm',
  'quantreg', 'rugarch', 'sampleSelection', 'strucchange', 'systemfit',
  'truncreg', 'tseries', 'vars'

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

Packages suggested but not available for checking:
  'DescTools', 'rjags', 'ggmcmc'

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

Packages suggested but not available for checking:
  'coin', 'R.rsp', 'latticeExtra', 'multcomp', 'mlmRev', 'MEMSS',
  'effects', 'ggbeeswarm', 'ggpubr', 'ggpol', 'glmmTMB', 'brms',
  'rstanarm', 'ez', 'ggResidpanel'

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: 'expm', 'Hmisc', 'ggrepel'

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: 'spatstat', 'spatstat.geom'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/afmToolkit.Rcheck/00install.out’ for details.
checkRd: (7) fDfPfunctions.Rd:23: \item in \arguments must have non-empty label
Package required but not available: ‘ivtools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'R2jags', 'rstpm2'

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

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: ‘glmnet’

Package suggested but not available for checking: ‘faraway’

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

Package suggested but not available for checking: ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/AgreementInterval.Rcheck/00install.out’ for details.
Packages required but not available: 'miscF', 'lme4', 'R2jags'

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.
Package required but not available: ‘klaR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'AER', 'agricolae', 'betareg', 'car', 'coin', 'effects',
  'equivalence', 'FrF2', 'gam', 'gstat', 'HH', 'latticeExtra', 'lme4',
  'mapproj', 'MCMCglmm', 'metafor', 'NADA', 'nullabor', 'pbkrtest',
  'rgdal', 'qicharts', 'SpATS', 'vcd'
Running examples in ‘agridat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: omer.sorghum
> ### Title: Multi-environment trial of sorghum, 6 environments
> ### Aliases: omer.sorghum
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> library(agridat)
> 
> data(omer.sorghum)
> dat <- omer.sorghum
> 
> # REML approach
> libs(lme4)
Installing package into ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
(as ‘lib’ is unspecified)
Warning in install.packages(p) :
  'lib = "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages"' is not writable
Error in install.packages(p) : unable to install packages
Calls: libs -> install.packages
Execution halted
Packages required but not available: 'lmerTest', 'pbkrtest'

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: 'raster', 'rgdal'

Package suggested but not available for checking: ‘rgeos’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xlsx', 'ggrepel', '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/agsemisc.Rcheck/00install.out’ for details.
Package required but not available: ‘seqinr’

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

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

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

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: ‘Biostrings’
Package unavailable to check Rd xrefs: ‘Biostrings’
'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: ‘unmarked’

Packages suggested but not available for checking:
  'betareg', 'coxme', 'fitdistrplus', 'glmmTMB', 'lme4', 'maxlike',
  'R2jags', 'R2WinBUGS', 'jagsUI', 'lmerTest'

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

Package suggested but not available for checking: ‘onewaytests’

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
Found the following files/directories:
  ‘ans_19-2.jpg’ ‘display2d_19-2.jpg’ ‘dist(3)_19-2.jpg’
  ‘dist(4)_19-2.jpg’ ‘dist(mirror)_19-2.jpg’ ‘dist(mirror2)_19-2.jpg’
Packages required but not available: 'SuperLearner', 'future.apply'

Package suggested but not available for checking: ‘tmle’

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

Packages suggested but not available for checking:
  'ggseas', 'mapproj', 'ggmap'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'caRamel', 'FME', 'ggmcmc', 'hydroPSO', 'Rmalschains', 'GGally'
Packages required but not available: 'dygraphs', 'xts'

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/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(aiRly)
  > 
  > test_check("aiRly")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_api.R:3:1): (code run outside of `test_that()`) ─────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'httptest'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test_api.R:3:0
   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 5 ]
  Error: Test failures
  Execution halted
Packages required but not available:
  'dygraphs', 'leaflet', 'MazamaCoreUtils', 'MazamaTimeSeries',
  'readr', 'xts'

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:
  'dygraphs', 'GGally', 'ggmap', 'leaflet', 'MazamaCoreUtils',
  'MazamaLocationUtils', 'MazamaSpatialUtils', 'openair', 'PWFSLSmoke',
  'readr', 'worldmet', 'xts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘stuve.pdf’
Packages required but not available: 'mirt', 'EstCRM'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
dke.fun.default: no visible global function definition for ‘hist’
kef: no visible global function definition for ‘dbinom’
kef: no visible global function definition for ‘dgamma’
kef: no visible global function definition for ‘dlnorm’
plot.dke.fun: no visible global function definition for ‘hist’
plot.dke.fun: no visible global function definition for ‘lines’
plot.hcvc.fun1d: no visible global function definition for
  ‘plot.default’
plot.hcvd.fun1d: no visible global function definition for
  ‘plot.default’
plot.kern.fun1d: no visible global function definition for
  ‘plot.default’
plot.kpmfe.fun1d: no visible global function definition for
  ‘plot.default’
plot.reg.fun1d: no visible global function definition for
  ‘plot.default’
simp_int: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dbinom dgamma dlnorm hist lines plot.default
Consider adding
  importFrom("graphics", "hist", "lines", "plot.default")
  importFrom("stats", "approx", "dbinom", "dgamma", "dlnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
‘library’ or ‘require’ call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
akmeans: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  kmeans
Consider adding
  importFrom("stats", "kmeans")
to your NAMESPACE file.
Packages required but not available: 'kml', '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/alabama.Rcheck/00install.out’ for details.
Packages required but not available:
  'airr', 'readr', 'seqinr', 'Biostrings', 'GenomicAlignments',
  'IRanges'

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

Packages which this enhances but not available for checking: 'eemR', 'EEM'

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.
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: 'caret', 'seqinr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'httptest'
'LazyData' is specified without a 'data' directory
Running ‘capture_util.R’ [0s/1s]
  Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(alfr)
  > 
  > test_check("alfr")
  Error in library(httptest) : there is no package called 'httptest'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'doParallel', 'org.Hs.eg.db', 'AnnotationDbi', 'readr'

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’
Package suggested but not available for checking: ‘pedigree’
Packages required but not available: 'vegan', 'BiodiversityR', 'adegenet'

Packages suggested but not available for checking:
  'poppr', 'GGally', 'ggforce', 'ggrepel', 'gggibbous', 'gganimate'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
batch.possSpells.fnc: no visible binding for global variable ‘words’
possSpells.fnc: no visible binding for global variable ‘len.phons’
possSpells.fnc: no visible binding for global variable ‘phon1’
possSpells.fnc: no visible binding for global variable ‘len.total’
possSpells.fnc: no visible binding for global variable ‘poss.spells’
Undefined global functions or variables:
  len.phons len.total phon1 poss.spells words
Found the following files/directories:
  ‘more.words.rda’ ‘more.words.txt’ ‘more.words_log.txt’
  ‘other.words.rda’ ‘other.words.txt’ ‘other.words_log.txt’
  ‘some.words.rda’ ‘some.words.txt’ ‘some.words_log.txt’
  ‘yet.more.words.rda’ ‘yet.more.words.txt’ ‘yet.more.words_log.txt’
Package suggested but not available for checking: ‘devtools’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dlookr', 'ggmosaic', 'party', 'unbalanced', 'glmnet'

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

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

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: ‘pedigree’

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

Package suggested but not available for checking: ‘alphahull’

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

Package suggested but not available for checking: ‘tidyquant’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Package required but not available: ‘car’

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: 'rjags', 'lme4', 'metafor'

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: 'ggmap', 'raster'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ALUES.Rcheck/00install.out’ for details.
Packages required but not available: 'ggrepel', 'readr', 'tidyverse'

Package suggested but not available for checking: ‘metaboliteIDmapping’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Biobase’
Malformed Description field: should contain one or more complete sentences.
EXP.step: no visible global function definition for ‘rgamma’
EXP.step: no visible global function definition for ‘rnorm’
MAX.step: no visible global function definition for ‘uniroot’
Norm.GMedian: no visible binding for global variable ‘median’
RNASeq.Data.Gene: no visible binding for global variable ‘quantile’
decom.initial: no visible global function definition for ‘kmeans’
decom.initial: no visible global function definition for ‘quantile’
decom.initial: no visible global function definition for ‘var’
dispersion.nb.QL: no visible binding for global variable ‘quantile’
est.mu.nb.mle: no visible global function definition for ‘runif’
est.v.nb.QL: no visible global function definition for ‘runif’
pdf2grid: no visible global function definition for ‘dnorm’
pdf2grid: no visible global function definition for ‘dgamma’
prior.grid: no visible global function definition for ‘sd’
prior.grid: no visible global function definition for ‘dnorm’
test.AMAP: no visible global function definition for ‘rgamma’
test.AMAP: no visible global function definition for ‘rnorm’
test.AMAP: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  dgamma dnorm kmeans median quantile rgamma rnorm runif sd uniroot var
Consider adding
  importFrom("stats", "dgamma", "dnorm", "kmeans", "median", "quantile",
             "rgamma", "rnorm", "runif", "sd", "uniroot", "var")
to your NAMESPACE file.
Rd file 'MGN.EM.Rd':
  \usage lines wider than 90 characters:
     MGN.EM(data, nK, p0 = NULL, d0 = 0, nK0 = 0, iter.max = 10, print.steps = FALSE, MGN0 = NULL, model = NULL, nMC = 10000)

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

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘fields’
Packages required but not available: 'raster', '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: ‘readr’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Zelig’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Amelia.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Package required but not available: ‘heatmaply’

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: ‘ProTrackR’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/AmigaFFH.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/aml.Rcheck/00install.out’ for details.
Packages required but not available: 'latticeExtra', 'msm', 'Hmisc'

Packages suggested but not available for checking: 'ggpubr', '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: ‘unmarked’

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

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: 'MplusAutomation', 'devtools'

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

Package suggested but not available for checking: ‘maptools’

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

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

Packages suggested but not available for checking:
  'adehabitatLT', 'adehabitatMA', 'ggraph', 'leaflet', 'moveHMM',
  'move', 'spacetime', 'trajectories', 'maptools'

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

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/AnaCoDa.Rcheck/00install.out’ for details.
Packages required but not available: 'car', 'fda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'vegan3d', 'analogue'

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

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

Package which this enhances but not available for checking: ‘SparkR’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/analysisPipelines.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Analyz.loadSteps,Analyz: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘BH-0.05-ListOfGenes.txt’ ‘BH-0.05-VM-ListOfGenes.txt’
  ‘CompleteListOfGenes.txt’ ‘GenesOutOfAnalysis.txt’
  ‘GenesOutOfAnalysis_NotEnoughObs.txt’
  ‘GenesOutOfAnalysis_NullVar.txt’ ‘VM-CompleteListOfGenes.txt’
  ‘bonferroni-0.05-ListOfGenes.txt’
  ‘bonferroni-0.05-VM-ListOfGenes.txt’
Packages required but not available: 'glmnet', 'selectiveInference'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
andrews: no visible global function definition for ‘plot.new’
andrews: no visible global function definition for ‘plot.window’
andrews: no visible global function definition for ‘title’
andrews: no visible global function definition for ‘axis’
andrews: no visible global function definition for ‘box’
andrews: no visible global function definition for ‘lines’
andrews: no visible global function definition for ‘rainbow’
andrews: no visible global function definition for ‘hsv’
selectand: no visible global function definition for ‘lines’
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window rainbow title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "title")
to your NAMESPACE file.
Package required but not available: ‘RSQLite’

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 required but not available: ‘raster’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'maptools', 'leaflet', 'leaflet.extras', 'rgdal', '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/animalTrack.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'devtools', 'Hmisc', 'mapproj', 'maptools'
Package required but not available: ‘imager’

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

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
Packages suggested but not available for checking: 'TruncatedNormal', 'tmg'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/anMC.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggpubr', 'Biobase'

Package suggested but not available for checking: ‘GEOquery’

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.
Packages required but not available: 'mc2d', 'tseries', 'fitdistrplus'

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

Packages suggested but not available for checking:
  'tidyverse', 'tidyquant', 'devtools'

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

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

Package suggested but not available for checking: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', '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/ANOVAreplication.Rcheck/00install.out’ for details.
Packages required but not available: 'DescTools', 'HH'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bit64', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'antaresRead', 'antaresProcessing', 'spMaps', 'dygraphs', 'plotly',
  'leaflet', 'rgeos', 'raster', 'geojsonio', 'leaflet.minicharts'

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

Package suggested but not available for checking: ‘survey’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'archetypes', 'depth', 'ICGE', 'biclust'

Package suggested but not available for checking: ‘calibrate’

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: ‘DescTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rglpk’
Running ‘testthat.R’ [102s/142s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > if (!requireNamespace("testthat", quietly = TRUE)) {
  +   stop("The `testthat` package is not available, therefore `anticlust` cannot be tested.")
  + }
  > 
  > library("anticlust")
  > library("testthat")
  > 
  > test_check("anticlust")
  [ FAIL 2 | WARN 0 | SKIP 6 | PASS 5816 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (6)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-objective-value.R:31:5): objective value for distance criterion is computed correctly ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'Rglpk'
  Backtrace:
      ▆
   1. ├─anticlust:::solve_ilp(ilp, "min") at test-objective-value.R:31:4
   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-solving-ilp.R:17:7): all levels of heuristicism work and that exact approach has best objective ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'Rglpk'
  Backtrace:
      ▆
   1. ├─anticlust:::exact_anticlustering(...) at test-solving-ilp.R:17:6
   2. │ └─anticlust:::solve_ilp(ilp, "min")
   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 6 | PASS 5816 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘competitiontoolbox’
Packages required but not available: 'mcclust', 'GGally'

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
Packages required but not available: 'readr', 'vroom'

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 suggested but not available for checking: ‘lme4’
Running examples in ‘aod-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: iccbin
> ### Title: Intra-Cluster Correlation for Binomial Data
> ### Aliases: iccbin show,iccbin-method
> ### Keywords: htest
> 
> ### ** Examples
> 
> 
> data(rats)
> tmp <- rats[rats$group == "TREAT", ]
> # A: glmm (model linearization)
> iccbin(n, y, data = tmp, method = "A")
Error in loadNamespace(x) : there is no package called ‘lme4’
Calls: iccbin ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: ‘lme4’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Aoptbdtvc.Rcheck/00install.out’ for details.
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:
  'rstan', 'BayesFactor', 'car', 'highcharter'

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: ‘MBESS’

Packages suggested but not available for checking: 'afex', 'ez'

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: apa.desc
> ### Title: Creates Mean (M) and Standard Deviation (SD) output with
> ###   confidence interval in APA style using Markdown.
> ### Aliases: apa.desc
> 
> ### ** Examples
> 
> #2-way ANOVA Example
> library(apaTables) #load apaTables to access goggles
Error in library(apaTables) : there is no package called ‘apaTables’
Execution halted
Packages required but not available: 'raster', 'FD'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (7) APResult-class.Rd:92-94: \item in \describe must have non-empty label
checkRd: (7) APResult-class.Rd:95-99: \item in \describe must have non-empty label
checkRd: (7) AggExResult-class.Rd:81-84: \item in \describe must have non-empty label
checkRd: (7) AggExResult-class.Rd:85-89: \item in \describe must have non-empty label
checkRd: (7) ExClust-class.Rd:69-71: \item in \describe must have non-empty label
checkRd: (7) ExClust-class.Rd:72-76: \item in \describe must have non-empty label
Packages required but not available: 'vegan', 'car'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'expm', 'phangorn'
Error(s) in re-building vignettes:
  ...
--- re-building ‘DrawingPhylogenies.Rnw’ using Sweave
--- finished re-building ‘DrawingPhylogenies.Rnw’

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

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

Error: processing vignette ‘RandomTopologies.Rnw’ failed with diagnostics:
 chunk 10 
Error in library(phangorn) : there is no package called ‘phangorn’

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

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'phangorn', 'adegenet'

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

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

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: ‘vcdExtra’
Error(s) in re-building vignettes:
  ...
--- re-building ‘aplore3-examples.Rnw’ using knitr
Quitting from lines 5-6 (./ch/glow.Rnw) 
Quitting from lines 8-8 (./ch/glow.Rnw) 
Error: processing vignette ‘aplore3-examples.Rnw’ failed with diagnostics:
there is no package called 'vcdExtra'
--- failed re-building ‘aplore3-examples.Rnw’

SUMMARY: processing the following file failed:
  ‘aplore3-examples.Rnw’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/APML0.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/apng.Rcheck/00install.out’ for details.
Packages required but not available: 'maxLik', 'randtoolbox', 'RSGHB'

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

Package suggested but not available for checking: ‘caret’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘optmatch’
Malformed Description field: should contain one or more complete sentences.
runAPSIM: warning in scan(reports_file[i], "", sep = "", skip =
  length(temp), nline = 1): partial argument match of ‘nline’ to
  ‘nlines’
runAPSIM: no visible global function definition for ‘write.table’
runAPSIM: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Package required but not available: ‘RSQLite’

Packages suggested but not available for checking:
  'BayesianTools', 'daymetr', 'FedData', 'GSODR', 'nasapower',
  'soilDB', 'spData'

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 required but not available: 'erer', 'car'

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 suggested but not available for checking: 'survey', 'srvyr'
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Quitting from lines 10-20 (./../man/rmdhunks/survey-example.Rmd) 
Quitting from lines NA-20 (./../man/rmdhunks/survey-example.Rmd) 
Error: processing vignette ‘intro.Rmd’ failed with diagnostics:
there is no package called 'srvyr'
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'openair', 'loa', 'strucchange', 'segmented'

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 suggested but not available for checking:
  'soilDB', 'latticeExtra', 'tactile', 'sharpshootR', 'markovchain',
  'Hmisc'
Packages required but not available: 'matlib', 'pedigree'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rgeos', 'rgdal', 'devtools'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/AQuadtree.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: 'rworldmap', 'rworldxtra'

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

Package suggested but not available for checking: ‘SMNCensReg’

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

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

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

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

Packages suggested but not available for checking: 'caret', 'gtsummary'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘vcd’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/archetypes.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: 'lidR', 'Rfast', 'VoxR'

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

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

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 required but not available: 'arules', 'R.utils'

Package suggested but not available for checking: ‘qCBA’

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.
ardec: no visible global function definition for ‘filter’
ardec.lm: no visible global function definition for ‘ar’
ardec.lm: no visible global function definition for ‘lm’
Undefined global functions or variables:
  ar filter lm
Consider adding
  importFrom("stats", "ar", "filter", "lm")
to your NAMESPACE file.
Packages required but not available: 'dynlm', 'lmtest', 'msm'

Packages suggested but not available for checking: 'qpcR', 'xts'

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

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

Packages suggested but not available for checking:
  'readr', 'marmap', '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: 'xts', '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 suggested but not available for checking:
  'arrow', 'R.utils', 'readr', 'RSQLite', 'duckdb', 'vroom',
  'future.apply'
Error(s) in re-building vignettes:
  ...
--- re-building ‘arkdb.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    ident, sql

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 59-61 (arkdb.Rmd) 
Error: processing vignette ‘arkdb.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 ‘arkdb.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'FAMT', 'VSURF', 'glmnet', 'doParallel', 'ComplexHeatmap'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Q.iid
> ### Title: Precision matrix for a IID process
> ### Aliases: Q.iid r.iid
> 
> ### ** Examples
> 
> require("leaflet")
Loading required package: leaflet
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘leaflet’
> require("sp")
Loading required package: sp
> 
> # simulate iid data and attach to spatial polygons data frame
> US.df@data$data <- c(r.iid(1, M=nrow(US.graph), sigma=1))
> 
> # color palette of data
> pal <- colorNumeric(palette="YlGnBu", domain=US.df@data$data)
Error in colorNumeric(palette = "YlGnBu", domain = US.df@data$data) : 
  could not find function "colorNumeric"
Execution halted
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Packages required but not available: 'np', 'Hmisc', 'spatstat.geom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'R.utils', 'aroma.core', 'R.oo', 'R.cache', 'R.devices',
  'R.filesets', 'aroma.apd'

Packages suggested but not available for checking:
  'Biobase', 'affy', 'affyPLM', 'aroma.light', 'gcrma', 'oligo',
  'oligoClasses', 'pdInfoBuilder'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'R.utils', 'aroma.core', 'R.oo', 'R.filesets', 'R.cache', 'PSCBS'

Packages suggested but not available for checking: 'aroma.light', 'GLAD'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'R.utils', 'R.filesets', 'R.devices', 'R.oo', 'R.cache', 'R.rsp',
  'PSCBS'

Packages suggested but not available for checking:
  'aroma.light', 'GLAD', 'sfit', 'expectile', 'HaarSeg', 'mpcbs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'alphashape3d', 'doParallel', 'geometry', 'Morpho', 'vegan'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘viridis’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘bit64’

Package suggested but not available for checking: ‘duckdb’

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

Packages suggested but not available for checking:
  'lmerTest', 'phia', 'DescTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘ARTP’
Package required but not available: ‘car’

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

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

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

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

Packages suggested but not available for checking: 'graph', 'Rgraphviz'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'gWidgets2', 'gWidgets2tcltk'

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: ‘Hmisc’
Packages required but not available: 'haven', 'readr', '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/asd.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spdep’
Package required but not available: ‘mixsqp’

Package suggested but not available for checking: ‘REBayes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'exact2x2', 'exactci', 'bpcp', 'coin'

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.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'BatchExperiments', 'BatchJobs', 'llama', 'mlr'

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 suggested but not available for checking: 'raster', 'sna'
Running examples in ‘asnipe-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: network_permutation
> ### Title: Perform Permutation
> ### Aliases: network_permutation
> 
> ### ** Examples
> 
> 
> ### USING TIMES, ETC.
> 
> data("group_by_individual")
> data("times")
> 
> # subset GBI (to reduce run time of the example)
> gbi <- gbi[,1:80]
> 
> ## define to 2 x N x N network to hold two association matrices
> networks <- array(0, c(2, ncol(gbi), ncol(gbi)))
> 
> ## calculate network for first half of the time
> networks[1,,] <- get_network(gbi, data_format="GBI", 
+ 	association_index="SRI", times=times, start_time=0, 
+ 	end_time=max(times)/2)
Generating  80  x  80  matrix
> networks[2,,] <- get_network(gbi, data_format="GBI",
+ 	association_index="SRI", times=times, 
+ 	start_time=max(times)/2, end_time=max(times))
Generating  80  x  80  matrix
> 
> ## calculate the weighted degree
> library(sna)
Error in library(sna) : there is no package called ‘sna’
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ASPBay.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: 'dae', 'doParallel'

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

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

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: ‘devtools’
'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’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'PerformanceAnalytics', 'quantmod', 'xts', 'riskParityPortfolio'

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

Package suggested but not available for checking: ‘klaR’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/AssotesteR.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘r2sundials’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/aster2.Rcheck/00install.out’ for details.
Packages required but not available: 'nanotime', 'onion'

Packages suggested but not available for checking:
  'asteRiskData', 'plotly', 'ggmap'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
beamDiskOverlap: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
fm_unred: no visible global function definition for ‘spline’
galage: no visible global function definition for ‘integrate’
lumdist: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate spline
Consider adding
  importFrom("stats", "integrate", "spline")
to your NAMESPACE file.
checkRd: (7) ten.Rd:23: \item in \value must have non-empty label
Package required but not available: ‘wavethresh’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Hmisc’
VPC.graph : findQuantile: no visible global function definition for
  ‘quantile’
VPC.graph : findQuantileCI : <anonymous>: no visible global function
  definition for ‘quantile’
asVPC.binW: no visible global function definition for ‘median’
asVPC.binW : <anonymous>: no visible global function definition for
  ‘quantile’
asVPC.binW: no visible global function definition for ‘quantile’
asVPC.distanceW: no visible global function definition for ‘median’
asVPC.distanceW : <anonymous>: no visible global function definition
  for ‘quantile’
asVPC.distanceW: no visible global function definition for ‘quantile’
makeCOVbin: no visible global function definition for ‘quantile’
makeCOVbin: no visible global function definition for ‘median’
read_Simdata: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  median quantile read.table
Consider adding
  importFrom("stats", "median", "quantile")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Packages suggested but not available for checking: 'haplo.stats', 'fields'
Running examples in ‘asymLD-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compute.ALD
> ### Title: Compute ALD.
> ### Aliases: compute.ALD
> 
> ### ** Examples
> 
> library(asymLD)
> 
> # An example using haplotype frequencies from Wilson(2010)
> data(hla.freqs)
> hla.a_b <- hla.freqs[hla.freqs$locus1=="A" & hla.freqs$locus2=="B",]
> compute.ALD(hla.a_b)
   ALD.x.y is asymmetric LD for locus x conditioned on locus y

  locus1 locus2       F.1    F.1.2        F.2     F.2.1   ALD.1.2   ALD.2.1
1      A      B 0.1021811 0.340332 0.04876543 0.1903394 0.5150291 0.3857872
> hla.freqs$locus <- paste(hla.freqs$locus1, hla.freqs$locus2, sep="-")
> compute.ALD(hla.freqs[hla.freqs$locus=="C-B",])
   ALD.x.y is asymmetric LD for locus x conditioned on locus y

  locus1 locus2        F.1     F.1.2        F.2     F.2.1   ALD.1.2   ALD.2.1
1      C      B 0.08637241 0.7350216 0.05040254 0.4520268 0.8425979 0.6503396
> # Note: additonal columns on the input dataframe (e.g., "locus" above) are allowed, but
> # ignored by the function.
> 
> # An example using genotype data from the haplo.stats package
> require(haplo.stats)
Loading required package: haplo.stats
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘haplo.stats’
> data(hla.demo)
Warning in data(hla.demo) : data set ‘hla.demo’ not found
> geno <- hla.demo[,5:8]  #DPB-DPA
Error: object 'hla.demo' not found
Execution halted
Packages required but not available: 'sn', 'gamlss.dist'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'forecast', 'stR', 'timeSeries', 'TSA', 'tseries', 'xts'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ata.Rcheck/00install.out’ for details.
get.est.ATT: no visible global function definition for ‘tail’
get.est.MT: no visible global function definition for ‘tail’
get.est.simple: no visible global function definition for ‘tail’
newton.r: no visible global function definition for ‘tail’
plot.ATE: no visible global function definition for ‘par’
plot.ATE: no visible global function definition for ‘axis’
plot.ATE: no visible global function definition for ‘abline’
plot.ATE: no visible global function definition for ‘lines’
plot.ATE: no visible global function definition for ‘legend’
plot.ATE: no visible global function definition for ‘points’
print.summary.ATE: no visible global function definition for
  ‘printCoefmat’
summary.ATE: no visible global function definition for ‘qnorm’
summary.ATE: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline axis legend lines par pnorm points printCoefmat qnorm tail
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "points")
  importFrom("stats", "pnorm", "printCoefmat", "qnorm")
  importFrom("utils", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'plotly', 'openair'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
atmcmc : rmvtnorm: no visible global function definition for ‘rnorm’
atmcmc: no visible global function definition for ‘rnorm’
atmcmc: no visible global function definition for ‘runif’
atmcmc: no visible global function definition for ‘par’
atmcmc: no visible global function definition for ‘lm’
atmcmc: no visible global function definition for ‘lines’
atmcmc: no visible global function definition for ‘var’
atmcmc: no visible global function definition for ‘cov’
atmcmc: no visible global function definition for ‘quantile’
atmcmc: no visible global function definition for ‘sd’
plotmcmc: no visible global function definition for ‘pdf’
plotmcmc: no visible global function definition for ‘par’
plotmcmc: no visible global function definition for ‘dev.new’
plotmcmc: no visible global function definition for ‘png’
plotmcmc: no visible global function definition for ‘hist’
plotmcmc: no visible global function definition for ‘dev.off’
plotmcmc: no visible global function definition for ‘lines’
Undefined global functions or variables:
  cov dev.new dev.off hist lines lm par pdf png quantile rnorm runif sd
  var
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf", "png")
  importFrom("graphics", "hist", "lines", "par")
  importFrom("stats", "cov", "lm", "quantile", "rnorm", "runif", "sd",
             "var")
to your NAMESPACE file.
Package required but not available: ‘msm’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
PlotAtm.lin : scale_image: no visible global function definition for
  ‘heat.colors’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘par’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘sd’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘approx’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘image’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘axis’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘mtext’
PlotAtm.lin: no visible global function definition for ‘arrows’
PlotAtm.lin: no visible global function definition for ‘text’
PlotAtm.lin: no visible global function definition for ‘polygon’
sky.colors: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  approx arrows axis heat.colors image mtext par polygon rgb sd text
Consider adding
  importFrom("grDevices", "heat.colors", "rgb")
  importFrom("graphics", "arrows", "axis", "image", "mtext", "par",
             "polygon", "text")
  importFrom("stats", "approx", "sd")
to your NAMESPACE file.
Rd file 'MakeArrivals.lin.Rd':
  \examples lines wider than 100 characters:
     MakeArrivals.lin(xs = c(100, 150), ys = c(100, 150), zs = c(100, 150), xr = 0, yr = 0, zr = 0, dt = 0.01, nt = 100, timing = c(0, 0), A ... [TRUNCATED]

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

These lines will be truncated in the PDF manual.
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 ‘ATNr.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘ATNr.Rmd’ using ‘UTF-8’... failed to complete the test
Package required but not available: ‘rdflib’

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

Package suggested but not available for checking: ‘trtf’

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: 'lme4', 'arm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/aucm.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/AUCRF.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/audiolyzR.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ggbeeswarm’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Freiburger.Rmd’ using rmarkdown
--- finished re-building ‘Freiburger.Rmd’

--- re-building ‘Intro_to_PTA_Standards.Rmd’ using rmarkdown
Quitting from lines 137-142 (Intro_to_PTA_Standards.Rmd) 
Error: processing vignette ‘Intro_to_PTA_Standards.Rmd’ failed with diagnostics:
there is no package called 'ggbeeswarm'
--- failed re-building ‘Intro_to_PTA_Standards.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘audio/libs/audio.so’:
  Found non-API call to R: ‘R_checkActivity’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages required but not available: 'ggrepel', 'hnp'

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

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: ‘multcomp’

Package suggested but not available for checking: ‘agricolae’

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

Package suggested but not available for checking: ‘unmarked’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ows4R’

Package suggested but not available for checking: ‘furrr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'vegan', 'mapdata', 'R.utils', 'maptools', 'jose', 'betapart'

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
Packages required but not available: 'caret', 'CORElearn', 'party'

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/autoCovariateSelection.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'fields', 'filehashSQLite', 'LatticeKrig'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Hmisc', 'ICBayes', 'icenReg', 'missForest', 'SurvRegCensCov',
  'rjags', 'coxme', 'mlr3'

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

Packages suggested but not available for checking: 'spatstat.geom', 'gear'

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: 'gstat', 'maptools'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'lme4', 'EBMAforecast', 'doParallel', 'doRNG', '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:
  'pamr', 'siggenes', 'annotate', 'org.Hs.eg.db',
  'ConsensusClusterPlus', 'clusterProfiler'

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

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 required but not available: ‘doParallel’

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

Packages suggested but not available for checking:
  'finalfit', 'lme4', 'TH.data', 'survminer', 'cmprsk', 'PairedData'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'broom.mixed', 'recipes', 'rsample', 'tune', 'framecleaner',
  'presenter', 'dials', 'readr', 'party', 'FOCI', 'glmnet'

Packages suggested but not available for checking:
  'moreparty', '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.
Packages required but not available:
  'maxLik', 'forecast', 'strucchange', 'doSNOW', 'lmtest', 'ggrepel'

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

Package suggested but not available for checking: ‘styler’

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

Packages suggested but not available for checking: 'caret', 'rpart.plot'

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

--- re-building ‘b_analyze-hass-cntry.Rmd’ using rmarkdown
--- finished re-building ‘b_analyze-hass-cntry.Rmd’

--- re-building ‘b_analyze-hass-region.Rmd’ using rmarkdown
Quitting from lines 95-122 (b_analyze-hass-region.Rmd) 
Error: processing vignette ‘b_analyze-hass-region.Rmd’ failed with diagnostics:
there is no package called 'ggrepel'
--- failed re-building ‘b_analyze-hass-region.Rmd’

--- re-building ‘b_analyze-hass.Rmd’ using rmarkdown
--- finished re-building ‘b_analyze-hass.Rmd’

SUMMARY: processing the following file failed:
  ‘b_analyze-hass-region.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'viridis', 'fields', 'haven', 'readODS'

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.
'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/aws.Rcheck/00install.out’ for details.
Packages required but not available: 'doParallel', 'QRM', 'MixAll'

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

Packages suggested but not available for checking: 'AzureRMR', 'AzureGraph'

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

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

Package suggested but not available for checking: ‘AzureKeyVault’

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

Packages suggested but not available for checking: 'AzureTableStor', 'odbc'

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

Package suggested but not available for checking: ‘AzureRMR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'jose', 'AzureRMR', 'AzureGraph', 'AzureAuth'

Package suggested but not available for checking: ‘AzureStor’

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

Packages suggested but not available for checking:
  'bit64', 'AzureGraph', 'AzureStor'

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

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

Package suggested but not available for checking: ‘AzureStor’

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

Packages suggested but not available for checking: 'AzureAuth', 'readr'

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

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

Package suggested but not available for checking: ‘AzureAuth’

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

Package suggested but not available for checking: ‘AzureKeyVault’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
CRexp_set: no visible global function definition for ‘runif’
b6e6rl: no visible global function definition for ‘runif’
derand_RL: no visible global function definition for ‘runif’
derandexp_RL: no visible global function definition for ‘runif’
nahvyb_expt: no visible global function definition for ‘runif’
roulete: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Skipping vignette re-building
Package suggested but not available for checking: ‘R.rsp’

VignetteBuilder package required for checking but not installed: ‘R.rsp’
.generateTransform: no visible global function definition for ‘sd’
.generateUnitHyperCube: no visible global function definition for
  ‘runif’
.makeBoundedSingleStep: no visible global function definition for
  ‘runif’
.makeBoundedStep: no visible global function definition for ‘runif’
.makeStep: no visible global function definition for ‘runif’
.staircaseSampling: no visible global function definition for ‘runif’
GaussianPrior: no visible global function definition for ‘qnorm’
LogNormalPrior: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm runif sd
Consider adding
  importFrom("stats", "qnorm", "runif", "sd")
to your NAMESPACE file.
Errors in running code in vignettes:
when running code in ‘comparing_distributions.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘comparing_distributions.Rmd’... failed to complete the test
Package required but not available: ‘edgeR’

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

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:
  'beautier', 'beastier', 'mauricer', 'phangorn'

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: 'SPOT', 'markovchain'

Packages suggested but not available for checking:
  'rpart.plot', 'simmer.plot', 'tidyverse'

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

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

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 suggested but not available for checking: 'fields', 'pcalg'
Error(s) in re-building vignettes:
  ...
--- re-building ‘exampleBackShift.Rmd’ using rmarkdown
Loading required package: backShift
Loading required package: ggplot2
Loading required package: fields
No id variables; using all as measure variables
Quitting from lines 269-272 (exampleBackShift.Rmd) 
Error: processing vignette ‘exampleBackShift.Rmd’ failed with diagnostics:
there is no package called 'fields'
--- failed re-building ‘exampleBackShift.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/backtest.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BACprior.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/BAEssd.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: ‘doSNOW’

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: 'rstan', 'forestplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘glmnet’
Packages required but not available:
  'C50', 'dials', 'earth', 'furrr', 'rsample'

Package suggested but not available for checking: ‘recipes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bahc.Rcheck/00install.out’ for details.
Packages required but not available:
  'rjags', 'R2jags', 'robCompositions', 'ggpubr'

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

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.
Package required but not available: ‘fields’

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: 'qrng', 'future.apply'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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(bambooHR)
  > 
  > test_check("bambooHR")
  Error in library(httptest) : there is no package called 'httptest'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Packages required but not available: 'rjags', 'R2jags'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ff', 'fields', 'gamlss', 'gamlss.dist', 'geoR', 'rjags', 'BayesX',
  'mapdata', 'maptools', 'spatstat', 'spdep', 'sdPrior', 'glogis',
  'glmnet'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bamlss.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BAMMtools.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: ‘gam’

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

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

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

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

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: 'lme4', 'tmle'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bartMachineJARs.Rcheck/00install.out’ for details.
Packages required but not available: 'bartMachineJARs', 'missForest'

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

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/Barycenter.Rcheck/00install.out’ for details.
Package required but not available: ‘pitchRx’

Packages suggested but not available for checking:
  'furrr', 'ggrepel', 'RSQLite'

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

Package suggested but not available for checking: ‘rms’

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

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 suggested but not available for checking:
  'gWidgets2', 'gWidgets2tcltk'
Packages required but not available: 'slippymath', 'raster', 'stars'

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

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.
Packages suggested but not available for checking:
  'Biobase', 'GO.db', 'GSEABase', 'org.Hs.eg.db', 'reactome.db'
'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: ‘Hmisc’

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.
Packages required but not available: 'Biostrings', 'rmcfs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BaSkePro.Rcheck/00install.out’ for details.
Packages required but not available:
  'ggrepel', 'sna', 'dendextend', 'GGally', 'ggnetwork', 'readr'

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

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: ‘GGally’
Error(s) in re-building vignettes:
  ...
--- re-building ‘BAS-vignette.Rmd’ using rmarkdown
Quitting from lines 266-272 (BAS-vignette.Rmd) 
Error: processing vignette ‘BAS-vignette.Rmd’ failed with diagnostics:
there is no package called 'GGally'
--- failed re-building ‘BAS-vignette.Rmd’

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

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

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

Packages which this enhances but not available for checking:
  'doMC', 'rPython'

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: 'BatchJobs', 'RSQLite'

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

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.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘quantreg’

Package suggested but not available for checking: ‘tidyverse’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'geometry', 'hypervolume', 'nls2', 'raster', 'vegan'

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

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

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

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

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: ‘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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘doParallel’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(bayesboot)
  > 
  > test_check("bayesboot")
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 0 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (2)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-bayesboot-deterministic.R:2:1): (code run outside of `test_that()`) ──
  <packageNotFoundError/error/condition>
  Error in `library(doParallel)`: there is no package called 'doParallel'
  Backtrace:
      ▆
   1. └─base::library(doParallel) at test-bayesboot-deterministic.R:2:0
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 0 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BayesBP.Rcheck/00install.out’ for details.
Package required but not available: ‘rstan’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rjags', 'forestplot', 'metafor', '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.
'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: ‘truncdist’

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

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: ‘MCMCpack’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bayesDccGarch.Rcheck/00install.out’ for details.
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 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.
Packages suggested but not available for checking: 'doMC', 'arm', 'lme4'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BayesFactor.Rcheck/00install.out’ for details.
Packages required but not available: 'forecast', 'rstan', 'prophet'

Package suggested but not available for checking: ‘ggfortify’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', '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/Bayesiangammareg.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘tmvtnorm’

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

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

Packages suggested but not available for checking:
  'devtools', 'recipes', 'rstan'

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:
  'emulator', 'tmvtnorm', 'msm', 'DHARMa'

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

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

Package suggested but not available for checking: ‘wpp2015’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lin_comb
> ### Title: Perform a linear combination of posterior samples
> ### Aliases: lin_comb
> 
> ### ** Examples
> 
> # data
> if (require(BGGM)) library(BGGM)
Loading required package: BGGM
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘BGGM’
> Y <- ptsd
Error: object 'ptsd' not found
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bayeslincom)
  > 
  > test_check("bayeslincom")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-lin_comb_methods.R:6:11): lin_comb methods produce expected errors ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'BGGM'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-lin_comb_methods.R:6:10
   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 1 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'ghyp', 'fAsianOptions', '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/bayesloglin.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bayeslongitudinal.Rcheck/00install.out’ for details.
Package required but not available: ‘PerMallows’

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: ‘tmvtnorm’

Package suggested but not available for checking: ‘tgp’

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

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BayesMixSurv.Rcheck/00install.out’ for details.
Packages required but not available:
  'furrr', 'MCMCpack', 'dygraphs', 'leaflet'

Packages suggested but not available for checking:
  'ggforce', 'xts', 'datamods', 'viridis'

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.
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 [112, 115] is out of the bounds [0, 112] of object ‘cbetaAllRow’ with type ‘arma::uvec’ {aka ‘arma::Col<unsigned int>’} [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bayesm.Rcheck/00install.out’ for details.
Package required but not available: ‘brms’

Package suggested but not available for checking: ‘rstan’

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

Packages suggested but not available for checking:
  'Rgraphviz', 'cyjShiny', 'qtlnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
noninform_prior : a : f1: no visible global function definition for
  ‘pbeta’
noninform_prior : a : f1: no visible global function definition for
  ‘dbeta’
noninform_prior : a: no visible global function definition for
  ‘integrate’
noninform_prior: no visible global function definition for ‘rbeta’
noninform_prior: no visible global function definition for ‘optim’
postNullFun : b : f1: no visible global function definition for ‘pbeta’
postNullFun : b : f1: no visible global function definition for ‘dbeta’
postNullFun : b: no visible global function definition for ‘integrate’
prior_prob : a : f1: no visible global function definition for ‘pbeta’
prior_prob : a : f1: no visible global function definition for ‘dbeta’
prior_prob : a: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  dbeta integrate optim pbeta rbeta
Consider adding
  importFrom("stats", "dbeta", "integrate", "optim", "pbeta", "rbeta")
to your NAMESPACE file.
Package required but not available: ‘StatMatch’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyverse', 'fda', 'gsDesign', 'madness', 'rjmcmc', 'R2jags',
  '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/BayesPieceHazSelect.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BayesPiecewiseICAR.Rcheck/00install.out’ for details.
Package required but not available: ‘gginnards’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggfortify', 'rstan', 'rstanarm', 'shinystan'
Packages required but not available:
  'bayesLife', 'MortCast', 'rworldmap', 'fields'

Package suggested but not available for checking: ‘wpp2015’

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

Package suggested but not available for checking: ‘rstan’

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: ‘rjags’

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: ‘rstanarm’

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BayesSAE.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘TeachingSampling’
Packages required but not available: 'rstan', 'lme4'

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

Package suggested but not available for checking: ‘spduration’

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

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: ‘smoothSurv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'BayesFactor', 'blavaan', 'brms', 'GGally', 'lme4', 'mediation',
  'rstan', 'rstanarm'
Packages suggested but not available for checking:
  'rworldmap', 'snowFT', 'rgdal', 'wpp2015'
Running ‘run_tests.R’ [1s/2s]
  Running ‘test_functions.R’ [0s/1s]
Running the tests in ‘tests/run_tests.R’ failed.
Complete output:
  > library(bayesTFR)
  > source('test_functions.R')
  > 
  > cran <- TRUE
  > for(wpp in rev(c(2010, 2012, 2015, 2017, 2019))) {
  + 	test.load.UNtfr(wpp)
  + 	test.load.UNlocations(wpp)
  + 	test.create.tfr.matrix(wpp)
  + }
  
  <=== Starting test of loading UN TFR file ====
  Loading required package: wpp2019
  
  ==== Test of loading UN TFR file OK.===>
  
  <=== Starting test of loading WPP location file ====
  
  ==== Test of loading WPP location file OK.===>
  
  <=== Starting test of loading WPP location file with my.locations.file ====
  
  ==== Test of loading WPP location file with my.locations.file OK.===>
  
  <=== Starting test of creating TFR matrix ====
  
  ==== Test of creating TFR matrix OK.===>
  
  <=== Starting test of loading UN TFR file ====
  Loading required package: wpp2017
  
  ==== Test of loading UN TFR file OK.===>
  
  <=== Starting test of loading WPP location file ====
  
  ==== Test of loading WPP location file OK.===>
  
  <=== Starting test of loading WPP location file with my.locations.file ====
  
  ==== Test of loading WPP location file with my.locations.file OK.===>
  
  <=== Starting test of creating TFR matrix ====
  
  ==== Test of creating TFR matrix OK.===>
  
  <=== Starting test of loading UN TFR file ====
  Loading required package: wpp2015
  Error in find.package(package, lib.loc, verbose = verbose) : 
    there is no package called 'wpp2015'
  Calls: test.load.UNtfr ... load.bdem.dataset -> do.call -> data -> find.package
  In addition: Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'wpp2015'
  Execution halted
Package required but not available: ‘rjags’

Packages suggested but not available for checking: 'rstan', 'BayesFactor'

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 suggested but not available for checking: 'tgp', 'bartMachine'
Package required but not available: ‘rjags’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘R2BayesX’
GNU make is a SystemRequirements.
Package required but not available: ‘rstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
‘library’ or ‘require’ call to ‘coda’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Rd file 'BPSpostSample.Rd':
  \usage lines wider than 90 characters:
     BPSpostSample(hyp, times, obs = NULL, mclen = 10, burnin = 0, thin = 1, df = 10, etastar = NULL)
  \examples lines wider than 100 characters:
     post<-BPSpostSample(hypars, times = earthquakes$ti, obs = earthquakes$ob, etastar = postmode$etastar)

These lines will be truncated in the PDF manual.
Found the following files/directories:
  ‘diagnostics.pdf’ ‘post.rda’
Packages required but not available: 'rjags', 'ArchaeoPhases'

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: ‘ggpubr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggfortify', 'lme4', '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/BAYSTAR.Rcheck/00install.out’ for details.
Packages required but not available: 'dataRetrieval', 'fitdistrplus'

Packages suggested but not available for checking: 'devtools', '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: ‘BGGM’
Package in Depends field not imported from: ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bbemkr.Rcheck/00install.out’ for details.
Package required but not available: ‘aws’

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: 'glmnet', 'Biostrings'
Error(s) in re-building vignettes:
  ...
--- re-building ‘article.Rnw’ using Sweave
Setting levels: control = No, case = Yes
Loading required package: glmnet
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'glmnet'
Installing package into '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages'
(as 'lib' is unspecified)
Warning in install.packages("glmnet") :
  ‘lib = "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages"’ is not writable

Error: processing vignette ‘article.Rnw’ failed with diagnostics:
 chunk 8 (label = glmnet) 
Error in install.packages("glmnet") : unable to install packages

--- failed re-building 'article.Rnw'

SUMMARY: processing the following file failed:
  'article.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'rms', 'AICcmodavg', 'Hmisc'
bbmm.contour: no visible global function definition for ‘na.omit’
bbmm.contour: no visible global function definition for ‘optimize’
bbmm.contour: no visible global function definition for ‘contour’
bbmm.contour: no visible global function definition for ‘points’
bbmm.contour: no visible global function definition for ‘lines’
brownian.bridge: no visible global function definition for ‘sd’
brownian.motion.variance: no visible global function definition for
  ‘optimize’
Undefined global functions or variables:
  contour lines na.omit optimize points sd
Consider adding
  importFrom("graphics", "contour", "lines", "points")
  importFrom("stats", "na.omit", "optimize", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: ‘geiger’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BBMV.Rcheck/00install.out’ for details.
bbo: no visible global function definition for ‘runif’
bbo: no visible global function definition for ‘tail’
Undefined global functions or variables:
  runif tail
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bbotk.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘Hmisc’
Packages required but not available: 'lme4', 'secr'

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

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: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘c3net’

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 ‘bcaboot.Rmd’ using rmarkdown
Quitting from lines 127-131 (bcaboot.Rmd) 
Error: processing vignette ‘bcaboot.Rmd’ failed with diagnostics:
Please install glmnet package for this vignette.
--- failed re-building ‘bcaboot.Rmd’

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

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

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

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

Package suggested but not available for checking: ‘biclust’

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

Packages suggested but not available for checking:
  'INLA', 'MCMCvis', 'plotly', 'rstan', 'R2jags', 'splancs'

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BCellMA.Rcheck/00install.out’ for details.
Package required but not available: ‘FME’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bcfrailph.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bcf.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bcgam.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: ‘ggforce’

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

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

Packages suggested but not available for checking:
  'future.apply', 'raster', 'rgdal', 'rgeos', 'stars'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bcpa.Rcheck/00install.out’ for details.
bcpmeta.model: no visible global function definition for ‘rbinom’
bcpmeta.model: no visible global function definition for ‘runif’
bcpmeta.parameters: no visible global function definition for ‘runif’
cp.plot: no visible global function definition for ‘postscript’
cp.plot: no visible global function definition for ‘lines’
cp.plot: no visible global function definition for ‘axis’
cp.plot: no visible global function definition for ‘box’
cp.plot: no visible global function definition for ‘points’
cp.plot: no visible global function definition for ‘dev.off’
lMarLik.EB.normAR: no visible global function definition for ‘optimize’
lMarLik.normAR: no visible global function definition for ‘integrate’
marginal.plot: no visible global function definition for ‘postscript’
marginal.plot: no visible global function definition for ‘axis’
marginal.plot: no visible global function definition for ‘box’
marginal.plot: no visible global function definition for ‘points’
marginal.plot: no visible global function definition for ‘dev.off’
simgen: no visible global function definition for ‘rnorm’
up.eta.MH.normAR: no visible global function definition for ‘runif’
up.eta.RS.normAR: no visible global function definition for ‘runif’
up.parameters.EB.normAR: no visible global function definition for
  ‘rnorm’
up.parameters.normAR: no visible global function definition for ‘rnorm’
up.parameters.normAR: no visible global function definition for ‘runif’
up.parameters.normAR: no visible global function definition for
  ‘rgamma’
Undefined global functions or variables:
  axis box dev.off integrate lines optimize points postscript rbinom
  rgamma rnorm runif
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "axis", "box", "lines", "points")
  importFrom("stats", "integrate", "optimize", "rbinom", "rgamma",
             "rnorm", "runif")
to your NAMESPACE file.
Packages suggested but not available for checking: 'strucchange', 'vegan'
Package required but not available: ‘odbc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'R2WinBUGS', 'rjags'
Package suggested but not available for checking: ‘webshot2’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bcROCsurface.Rcheck/00install.out’ for details.
Packages required but not available: 'mcclust', 'nFactors'

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

Packages suggested but not available for checking:
  'batchelor', 'kBET', 'scater', 'lisi', 'harmony', 'dlfUtils'

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

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

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

Packages suggested but not available for checking:
  'doParallel', 'duckdb', 'rangeBuilder', 'raster'

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/bde.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'ssgraph', 'tmvtnorm'
Packages required but not available: 'GenOrd', 'MultiOrd', 'RSQLite'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bdots.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BDP2.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: ‘rjags’

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

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

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

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

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

Packages suggested but not available for checking:
  'beadarrayExampleData', 'lumi'

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

Package suggested but not available for checking: ‘flowCore’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘vioplot’
Error(s) in re-building vignettes:
  ...
--- re-building ‘beanplot.Rnw’ using Sweave

Error: processing vignette ‘beanplot.Rnw’ failed with diagnostics:
 chunk 4 (label = singers) 
Error in library("vioplot") : there is no package called ‘vioplot’

--- failed re-building ‘beanplot.Rnw’

SUMMARY: processing the following file failed:
  ‘beanplot.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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bea.R.Rcheck/00install.out’ for details.
Packages required but not available:
  'beautier', 'devtools', 'phangorn', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘beast_plot_toy.pdf’
Package required but not available: ‘seqinr’

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

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

Packages suggested but not available for checking: 'biomaRt', 'GEOquery'

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

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.
Found the following files/directories:
  ‘alist.txt’ ‘rpkg’
Packages required but not available: 'DiagrammeR', 'ufs', '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/behavr.Rcheck/00install.out’ for details.
Packages required but not available:
  'expm', 'ggfortify', 'xts', 'forecast', 'future.apply'

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:
  'raster', 'rgdal', 'rasterVis', 'stars'
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(belg)
  > 
  > test_check("belg")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 19 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-raster-stars.R:3:1): (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-raster-stars.R:3:0
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 19 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘belg1.Rmd’ using rmarkdown
Quitting from lines 13-32 (belg1.Rmd) 
Error: processing vignette ‘belg1.Rmd’ failed with diagnostics:
there is no package called 'rasterVis'
--- failed re-building ‘belg1.Rmd’

SUMMARY: processing the following file failed:
  ‘belg1.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'magic', '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/Benchmarking.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘benchmarkme’
Package required but not available: ‘doParallel’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.bench_mark
> ### Title: Autoplot method for bench_mark objects
> ### Aliases: autoplot.bench_mark plot.bench_mark
> 
> ### ** Examples
> 
> dat <- data.frame(x = runif(10000, 1, 1000), y=runif(10000, 1, 1000))
> 
> res <- bench::mark(
+   dat[dat$x > 500, ],
+   dat[which(dat$x > 500), ],
+   subset(dat, x > 500))
> 
> if (require(ggplot2) && require(tidyr)) {
+ 
+   # Beeswarm plot
+   autoplot(res)
+ 
+   # ridge (joyplot)
+   autoplot(res, "ridge")
+ 
+   # If you want to have the plots ordered by execution time you can do so by
+   # ordering factor levels in the expressions.
+   if (require(dplyr) && require(forcats)) {
+ 
+     res %>%
+       mutate(expression = forcats::fct_reorder(as.character(expression), min, .desc = TRUE)) %>%
+       as_bench_mark() %>%
+       autoplot("violin")
+   }
+ }
Loading required package: ggplot2
Loading required package: tidyr
Error: `ggbeeswarm` must be installed to use `type = "beeswarm"` option.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'benthos', '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 required but not available: ‘rtf’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'gstat', 'vioplot', 'spatstat.geom'
Package required but not available: ‘Rmpfr’

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: ‘glmnet’

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

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

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

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 required but not available: ‘betareg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘raster’
'LazyData' is specified without a 'data' directory
Checking should be performed on sources prepared by ‘R CMD build’.
Packages required but not available:
  'geometry', 'picante', 'doSNOW', 'itertools'

Package suggested but not available for checking: ‘vegan’

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.
Package required but not available: ‘vegan’

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

Packages suggested but not available for checking:
  'car', 'partykit', 'strucchange'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/betategarch.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
Packages required but not available:
  'plotly', 'forecast', 'dygraphs', 'RMySQL', 'sqldf'

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

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: ‘forecast’

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

Package suggested but not available for checking: ‘raster’

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

Packages suggested but not available for checking: 'metafor', 'lmtest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'doBy', 'Hmisc'
Packages required but not available:
  'DescTools', 'spdep', 'maptools', 'rgdal', 'rgeos'

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: 'symDMatrix', 'ff'

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

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bggAnalytics.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'BFpack', 'GGally', 'sna'

Package suggested but not available for checking: ‘networktools’

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: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
block.gibbs: no visible global function definition for ‘rmultinom’
rdirichlet: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  rgamma rmultinom
Consider adding
  importFrom("stats", "rgamma", "rmultinom")
to your NAMESPACE file.
Packages required but not available: 'EDISON', 'glmnet'

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

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: ‘MCMCpack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
global: no visible global function definition for ‘par’
global: no visible global function definition for ‘runif’
global: no visible global function definition for ‘cov’
mymcmc: no visible global function definition for ‘par’
mymcmc: no visible global function definition for ‘rnorm’
mymcmc: no visible global function definition for ‘runif’
mymcmc: no visible global function definition for ‘cov’
mymcmc: no visible global function definition for ‘lines’
plkhci: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  cov lines par qchisq rnorm runif
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "cov", "qchisq", "rnorm", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: ‘FrF2’
Packages required but not available: 'doRNG', 'R2jags'

Package suggested but not available for checking: ‘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/bhm.Rcheck/00install.out’ for details.
Package required but not available: ‘wavethresh’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘bibliometrix’
Packages required but not available:
  'factoextra', 'FactoMineR', 'ggrepel', 'plotly', 'readr'

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

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

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.
Packages required but not available: 'graph', 'Rgraphviz', 'RBGL', 'pcalg'

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 required but not available:
  'RPostgreSQL', 'rgeos', 'rgdal', 'fasterize', 'raster', 'doParallel'

Package suggested but not available for checking: ‘maptools’

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

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

Packages suggested but not available for checking:
  'lavaan.survey', 'survey', 'TAM'

Packages which this enhances but not available for checking:
  'Hmisc', 'intsvy', 'LSAmitR'

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

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

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.
Packages required but not available: 'bigstatsr', 'furrr'

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

Packages suggested but not available for checking: 'INLA', 'tmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fields’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bigGP.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘glmnet’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/biglasso.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘RSQLite’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/biglmm.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘RSQLite’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/biglm.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Packages which this enhances but not available for checking:
  'biganalytics', 'bigtabulate'
Found the following significant warnings:
  bigmemory.cpp:971:33: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  bigmemory.cpp:995:36: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  bigmemory.cpp:1019:33: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bigmemory.Rcheck/00install.out’ for details.
checkRd: (7) attach.big.matrix.Rd:74: invalid email address: <bigmemoryauthors@gmail.com>
checkRd: (7) big.matrix-class.Rd:104: invalid email address: <bigmemoryauthors@gmail.com>
checkRd: (7) big.matrix.Rd:279: invalid email address: <bigmemoryauthors@gmail.com>
checkRd: (7) morder.Rd:84: invalid email address: <bigmemoryauthors@gmail.com>
checkRd: (7) mwhich.Rd:99: invalid email address: <bigmemoryauthors@gmail.com>
checkRd: (7) write.big.matrix.Rd:179: invalid email address: <bigmemoryauthors@gmail.com>
Checking should be performed on sources prepared by ‘R CMD build’.
Package required but not available: ‘doParallel’

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

Package suggested but not available for checking: ‘SKAT’

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

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/bigReg.Rcheck/00install.out’ for details.
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.
Packages required but not available:
  'bigstatsr', 'bigparallelr', 'bigsparser', 'bigutilsr', 'rmio'

Packages suggested but not available for checking:
  'gaston', 'Hmisc', 'pcadapt', 'RSQLite', 'R.utils'

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

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

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

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

Package suggested but not available for checking: ‘devtools’

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: ‘biganalytics’

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

Package suggested but not available for checking: ‘rrcov’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘ccf_ccf_ID31_ID32_res.jpg’ ‘ccf_ccf_ID31_ID32_res.pdf’
  ‘output_ENSO_NHSST.tmp’ ‘plot_plot_ts_RAW_BIN_enso_sst.pdf’
  ‘plot_plot_ts_RAW_BIN_enso_sst01.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst02.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst03.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst04.png’ ‘plot_ts_ACER_ABRUPT.pdf’
  ‘plot_ts_ACER_ABRUPT01.png’ ‘plot_ts_ACER_ABRUPT02.png’
  ‘plot_ts_ACER_ABRUPT03.png’ ‘plot_ts_ACER_ABRUPT04.png’
  ‘salida_ACER_ABRUPT.tmp’ ‘scaterplot_scatterplot_ENSO_SST.jpg’
  ‘scaterplot_scatterplot_ENSO_SST.pdf’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/binda.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'gamlss', 'gamlss.cens', 'gamlss.dist'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘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/BinNonNor.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BinNor.Rcheck/00install.out’ for details.
bin_ps: no visible global function definition for ‘runif’
bin_ps: no visible global function definition for ‘dbinom’
draw_i: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbinom runif
Consider adding
  importFrom("stats", "dbinom", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: ‘correlbinom’
Running examples in ‘binomialRF-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: binomialRF
> ### Title: random forest feature selection based on binomial exact test
> ### Aliases: binomialRF
> 
> ### ** Examples
> 
> set.seed(324)
> 
> ###############################
> ### Generate simulation data
> ###############################
> 
> X = matrix(rnorm(1000), ncol=10)
> trueBeta= c(rep(10,5), rep(0,5))
> z = 1 + X %*% trueBeta
> pr = 1/(1+exp(-z))
> y = as.factor(rbinom(100,1,pr))
> 
> ###############################
> ### Run binomialRF
> ###############################
> require(correlbinom)
Loading required package: correlbinom
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘correlbinom’
> 
> rho = 0.33
> ntrees = 250
> cbinom = correlbinom(rho, successprob =  calculateBinomialP(10, .5), trials = ntrees, 
+                                precision = 1024, model = 'kuk')
Error in correlbinom(rho, successprob = calculateBinomialP(10, 0.5), trials = ntrees,  : 
  could not find function "correlbinom"
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Loading required package: correlbinom
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'correlbinom'
Quitting from lines 92-99 (my-vignette.Rmd) 
Error: processing vignette ‘my-vignette.Rmd’ failed with diagnostics:
could not find function "correlbinom"
--- failed re-building ‘my-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
IndivdRUMIndMH: no visible global function definition for
  ‘flush.console’
dRUMAuxMix: no visible global function definition for ‘flush.console’
dRUMHAM: no visible global function definition for ‘flush.console’
dRUMIndMH: no visible global function definition for ‘flush.console’
print.binomlogit: no visible global function definition for ‘is’
summary.binomlogit: no visible global function definition for ‘is’
Undefined global functions or variables:
  flush.console is
Consider adding
  importFrom("methods", "is")
  importFrom("utils", "flush.console")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Description field: should contain one or more complete sentences.
‘library’ or ‘require’ calls in package code:
  ‘ggplot2’ ‘lattice’ ‘polynom’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/binomSamSize.Rcheck/00install.out’ for details.
Packages required but not available: 'GenOrd', 'OrdNor'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'edgeR', 'Rsamtools', 'GenomicAlignments', 'GenomicRanges',
  'IRanges', 'csaw', 'SummarizedExperiment', 'S4Vectors', 'RMySQL'

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_earthbreaks
> ### Title: Create breaks using earth (i.e. MARS)
> ### Aliases: create_earthbreaks
> 
> ### ** Examples
> 
> earth_breaks <- create_breaks(x=iris$Sepal.Length, y=iris$Sepal.Width, method="earth")
Error in create_earthbreaks(x, y, control = control) : 
  Please install earth: install.packages('earth')
Calls: create_breaks -> create_earthbreaks
Execution halted
Package required but not available: ‘rstan’

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

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

Packages suggested but not available for checking:
  'vegan3d', 'car', 'effects', 'multcomp', 'splancs', 'dismo',
  'raster', 'rgdal', 'maxlike', 'gam', 'earth', 'mda', 'glmnet',
  'maptools', 'ENMeval', 'red', 'rgeos', 'Rlof', 'maxnet', 'party',
  'blockCV', 'envirem'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'maxLik', 'mixtools', '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/BIOdry.Rcheck/00install.out’ for details.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Found the following files/directories:
  ‘Plots.pdf’
Packages required but not available: 'raster', 'maptools', 'vegan'

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/biogram.Rcheck/00install.out’ for details.
Package required but not available: ‘FME’

Package suggested but not available for checking: ‘tidyverse’

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

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

Package suggested but not available for checking: ‘biomaRt’

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

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

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

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

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

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

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: 'agricolae', 'predictmeans'

Packages which this enhances but not available for checking:
  'asreml', 'lme4', 'sommer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'raster', 'rasterVis', 'mda', 'dismo', 'caret', 'ENMeval',
  'doParallel', 'earth', 'maxnet'

Packages suggested but not available for checking:
  'Hmisc', 'gam', 'ecospat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘MGRASTer’
‘library’ or ‘require’ call to ‘MGRASTer’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for ‘packageVersion’
biom.matrix: no visible global function definition for ‘packageVersion’
Undefined global functions or variables:
  packageVersion
Consider adding
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
checkRd: (7) bionetdata-package.Rd:29: invalid email address: {valentini,re}@di.unimi.it
Packages required but not available:
  'FME', 'bioinactivation', 'MEIGOR', 'tidyverse'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Bios2cor.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bios2mds.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:
  'cobs', 'devtools', 'glmnet', 'mboost', 'plsRcox', 'survAUC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'car', 'bshazard', 'rstpm2', 'Epi'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/biostat3.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘car’
Packages required but not available:
  'doParallel', 'ks', 'picante', 'raster', 'rgdal', 'rgeos',
  'spatstat.geom', 'vegan'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'bipartite', 'vegan'
Running examples in ‘bipartiteD3-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Matrix2DF
> ### Title: Convert a bipartite-style matrix to dataframe
> ### Aliases: Matrix2DF
> 
> ### ** Examples
> 
> 
> data(Safariland, package='bipartite')
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘bipartite’
Calls: data -> find.package
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bipartiteD3_Intro.Rmd’ using rmarkdown
Quitting from lines 14-23 (bipartiteD3_Intro.Rmd) 
Error: processing vignette ‘bipartiteD3_Intro.Rmd’ failed with diagnostics:
there is no package called 'bipartite'
--- failed re-building ‘bipartiteD3_Intro.Rmd’

SUMMARY: processing the following file failed:
  ‘bipartiteD3_Intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'vegan', 'sna', 'fields'

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

Packages suggested but not available for checking:
  'dclone', 'R2WinBUGS', 'micemd', 'miceadds'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggrepel’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BiplotML.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘sampleSelection’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BiProbitPartial.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/birankr.Rcheck/00install.out’ for details.
Packages required but not available:
  'ks', 'raster', 'rgdal', 'rgeos', 'rworldmap', 'rworldxtra'

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: ‘sirt’
Running examples in ‘bisect-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bisect_semi_suprevised
> ### Title: Add together two numbers.
> ### Aliases: bisect_semi_suprevised
> 
> ### ** Examples
> 
> ## Randomly choose samples to be used as known
> n_known_samples <- 50
> known_samples_indices <- sample.int(nrow(baseline_GSE40279), size = n_known_samples)
> known_samples <- as.matrix(baseline_GSE40279[known_samples_indices, ])
> 
> ## Fit a dirichlet distribution to known samples to use as prior
> fit_dirichlet <- sirt::dirichlet.mle(as.matrix(known_samples))
Error in loadNamespace(x) : there is no package called ‘sirt’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bisect_vignette.Rmd’ using rmarkdown
Quitting from lines 122-125 (bisect_vignette.Rmd) 
Error: processing vignette ‘bisect_vignette.Rmd’ failed with diagnostics:
there is no package called 'sirt'
--- failed re-building ‘bisect_vignette.Rmd’

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

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

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

Packages suggested but not available for checking: 'GO.db', 'org.Hs.eg.db'

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

Package suggested but not available for checking: ‘fields’

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

Package suggested but not available for checking: ‘Seurat’

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/bit64.Rcheck/00install.out’ for details.
Packages required but not available: 'phytools', 'vioplot'

Package suggested but not available for checking: ‘mvMORPH’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'httptest', 'tidyquant'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bitmexr)
  > 
  > 
  > test_check("bitmexr")
  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 ‘authentication.Rmd’ using rmarkdown
--- finished re-building ‘authentication.Rmd’

--- re-building ‘getting-started.Rmd’ using rmarkdown
--- finished re-building ‘getting-started.Rmd’

--- re-building ‘placing-orders.Rmd’ using rmarkdown
--- finished re-building ‘placing-orders.Rmd’

--- re-building ‘trade-data.Rmd’ using rmarkdown
Quitting from lines 11-17 (trade-data.Rmd) 
Error: processing vignette ‘trade-data.Rmd’ failed with diagnostics:
there is no package called 'httptest'
--- failed re-building ‘trade-data.Rmd’

SUMMARY: processing the following file failed:
  ‘trade-data.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'bit64', 'ff'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BiTrinA.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘compound.Cox’

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

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

Package suggested but not available for checking: ‘devtools’

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: ‘DHARMa’

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: 'bkmr', 'rstan'

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

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

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:
  'basecamb', 'survAUC', 'DescTools', 'Hmisc'

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.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/blatent.Rcheck/00install.out’ for details.
Packages required but not available: 'MCMCpack', 'rstan', 'future.apply'

Packages suggested but not available for checking:
  'modeest', 'rjags', 'semTools'

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

Package suggested but not available for checking: ‘sn’

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/Blendstat.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/blink.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: 'arm', '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 required but not available: ‘rtkore’

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

Packages suggested but not available for checking:
  'automap', 'rgeos', 'rgdal', 'future.apply'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
blockMessage : <anonymous>: no visible global function definition for
  ‘head’
blockMessage: no visible global function definition for ‘head’
blockMessage: no visible global function definition for ‘tail’
Undefined global functions or variables:
  head tail
Consider adding
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'sna', 'doRNG', 'doParallel'
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: ‘maxLik’

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: ‘randtoolbox’

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BLRPM.Rcheck/00install.out’ for details.
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: ‘readr’

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.
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 ‘nMaxCritMet’ with type ‘arma::rowvec’ {aka ‘arma::Row<double>’} [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bmabasket.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BMAmevt.Rcheck/00install.out’ for details.
Package required but not available: ‘rrcov’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Amelia', 'snowfall', 'rsem', 'sem'

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: 'Amelia', 'snowfall', 'sem'

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: blockBootSample
> ### Title: Block Bootstrap
> ### Aliases: blockBootSample
> 
> ### ** Examples
> 
> data(LaborSupply, package="plm")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘plm’
Calls: data -> find.package
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Bmix.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bmk.Rcheck/00install.out’ for details.
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.
Malformed Description field: should contain one or more complete sentences.
bmmix : LL.y: no visible global function definition for ‘dmultinom’
bmmix : LL.x : <anonymous>: no visible global function definition for
  ‘dmultinom’
bmmix : LPrior.alpha: no visible global function definition for ‘dexp’
bmmix : alpha.move: no visible global function definition for ‘rnorm’
bmmix : alpha.move: no visible global function definition for ‘runif’
bmmix : phi.move: no visible global function definition for ‘rnorm’
bmmix : phi.move: no visible global function definition for ‘runif’
bmmix: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  dexp dmultinom read.table rnorm runif
Consider adding
  importFrom("stats", "dexp", "dmultinom", "rnorm", "runif")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘mcmc.txt’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BMRBr.Rcheck/00install.out’ for details.
Packages required but not available:
  'fields', 'gsubfn', 'MCMCpack', 'mhsmm', 'multicool'

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: ‘rstan’

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

Packages suggested but not available for checking:
  'INLA', 'ggrepel', 'ggspatial', 'ggsn', 'ggpubr', 'inlabru'

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

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

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.
Packages suggested but not available for checking:
  'graph', 'gRain', 'gRbase', 'mlr', 'Rgraphviz'
Error(s) in re-building vignettes:
  ...
--- re-building ‘methods.Rmd’ using rmarkdown
--- finished re-building ‘methods.Rmd’

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

--- re-building ‘usage.rmd’ using rmarkdown
Quitting from lines 121-122 (usage.rmd) 
Error: processing vignette ‘usage.rmd’ failed with diagnostics:
Package graph needed 
--- failed re-building ‘usage.rmd’

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

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
make_topology: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package required but not available: ‘np’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: arc.strength
> ### Title: Measure arc strength
> ### Aliases: arc.strength boot.strength custom.strength bf.strength
> ###   mean.bn.strength averaged.network inclusion.threshold
> ### Keywords: network scores independence tests structure learning
> 
> ### ** Examples
> 
> data(learning.test)
> res = hc(learning.test)
> arc.strength(res, learning.test)
  from to   strength
1    A  B -1153.8796
2    A  D -1938.9499
3    C  D  -823.7605
4    B  E  -720.8266
5    F  E  -549.2300
> 
> ## Not run: 
> ##D arcs = boot.strength(learning.test, algorithm = "hc")
> ##D arcs[(arcs$strength > 0.85) & (arcs$direction >= 0.5), ]
> ##D averaged.network(arcs)
> ##D 
> ##D start = random.graph(nodes = names(learning.test), num = 50)
> ##D netlist = lapply(start, function(net) {
> ##D   hc(learning.test, score = "bde", iss = 10, start = net) })
> ##D arcs = custom.strength(netlist, nodes = names(learning.test),
> ##D          cpdag = FALSE)
> ##D arcs[(arcs$strength > 0.85) & (arcs$direction >= 0.5), ]
> ##D modelstring(averaged.network(arcs))
> ## End(Not run)
> 
> bf.strength(res, learning.test, score = "bds", prior = "marginal")
Loading required namespace: Rmpfr
Failed with error:  ‘there is no package called ‘Rmpfr’’
Error in check.and.load.package("Rmpfr") : 
  this function requires the Rmpfr package.
Calls: bf.strength -> check.and.load.package
Execution halted
Package required but not available: ‘rjags’

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

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

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

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

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

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

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/BNPTSclust.Rcheck/00install.out’ for details.
Packages required but not available: 'glmnet', 'graph'

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

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

Package suggested but not available for checking: ‘np’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'graph', 'Rgraphviz', 'qgraph'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bnstruct.Rcheck/00install.out’ for details.
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 suggested but not available for checking: ‘cytofan’
Error(s) in re-building vignettes:
  ...
--- re-building ‘bodenmiller.Rmd’ using rmarkdown
Quitting from lines 13-24 (bodenmiller.Rmd) 
Error: processing vignette ‘bodenmiller.Rmd’ failed with diagnostics:
there is no package called 'cytofan'
--- failed re-building ‘bodenmiller.Rmd’

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

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

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: 'future.apply', 'gamlr', 'glmnet'

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

Package suggested but not available for checking: ‘ijtiff’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BonEV.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BoolFilter.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘attractors.tex’ ‘cellcycle.sbml’ ‘cellcycle.txt’ ‘pajek_export.net’
  ‘sequence.txt’ ‘testNet.bn’
Package required but not available: ‘styler’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ARDL', 'dynamac', 'vars', 'ggfortify', 'fBasics'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'IsingFit', 'qgraph', 'IsingSampler', 'mgm', 'NetworkToolbox',
  'networktools'

Packages suggested but not available for checking:
  'GGMncv', 'graphicalVAR', 'relaimpo'

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

Package suggested but not available for checking: ‘plsdof’

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: 'car', '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/bootspecdens.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bootStepAIC.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'doMC', 'doParallel'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BootstrapQTL.Rcheck/00install.out’ for details.
Package required but not available: ‘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/boottol.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Boptbd.Rcheck/00install.out’ for details.
Package required but not available: ‘R2jags’

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.
Packages suggested but not available for checking:
  'cplexAPI', 'glmnet', 'ggpubr', 'devtools', 'bestsubset'
Error(s) in re-building vignettes:
  ...
--- re-building ‘BOSO.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: 'kableExtra'

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

    group_rows

Quitting from lines 21-29 (BOSO.Rmd) 
Error: processing vignette ‘BOSO.Rmd’ failed with diagnostics:
there is no package called 'glmnet'
--- failed re-building ‘BOSO.Rmd’

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

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

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

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

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.
Rd file 'beq.lin.Rd':
  \examples lines wider than 100 characters:
     plot(x,h_sol0,type="l",lty=1,main=paste("Water Surface Elevetion after",t,"days",sep=" "),xlab="x[m]",ylab="h[m]")

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

These lines will be truncated in the PDF manual.
Package required but not available: ‘metafor’

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.
Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'bit64', 'rio'

Package suggested but not available for checking: ‘jose’

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/bpca.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bpcp.Rcheck/00install.out’ for details.
Packages required but not available: 'rstan', 'shinystan'

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

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

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

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/bpp.Rcheck/00install.out’ for details.
Package required but not available: ‘NPflow’

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

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

Package suggested but not available for checking: ‘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/braidReports.Rcheck/00install.out’ for details.
Packages required but not available: 'devtools', 'rolocISCCNBS'

Package suggested but not available for checking: ‘ggfortify’

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: ‘doParallel’

Packages suggested but not available for checking:
  'Hmisc', 'RGtk2', 'cairoDevice', 'car', 'expm', 'ggrepel',
  'mediation'

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

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

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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bread.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/breakage.Rcheck/00install.out’ for details.
Packages required but not available: 'lme4', 'phyloseq'

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

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

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

Package suggested but not available for checking: ‘breathteststan’

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

Packages suggested but not available for checking:
  'shinystan', 'breathtestcore'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'R2jags', 'rjags', 'R.rsp', 'BayesFactor', 'rstan', 'rstanarm',
  'MCMCpack'

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

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

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

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

... incomplete output.  Crash?

  ‘bridgesampling_example_jags.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘bridgesampling_example_nimble.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘bridgesampling_example_stan.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘bridgesampling_stan_ttest.Rmd’ using ‘UTF-8’... failed to complete the test
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/briKmeans.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: ‘GGally’

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(briqr)
  > 
  > test_check("briqr")
  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/BRISC.Rcheck/00install.out’ for details.
Packages required but not available:
  'fasterize', 'raster', 'rgdal', 'rgeos'

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

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

Package suggested but not available for checking: ‘betareg’

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

Packages suggested but not available for checking:
  'cmdstanr', 'projpred', 'rtdists', 'spdep', 'lme4', 'MCMCglmm',
  'arm', '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/brnn.Rcheck/00install.out’ for details.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘AGD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'gghighlight', 'lme4', 'readr'
Running examples in ‘brolgar-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: monotonic
> ### Title: Are values monotonic? Always increasing, decreasing, or
> ###   unvarying?
> ### Aliases: monotonic increasing decreasing unvarying
> 
> ### ** Examples
> 
> vec_inc <- c(1:10)
> vec_dec<- c(10:1)
> vec_ran <- c(sample(1:10))
> vec_flat <- rep.int(1,10)
> 
> increasing(vec_inc)
[1] TRUE
> increasing(vec_dec)
[1] FALSE
> increasing(vec_ran)
[1] FALSE
> increasing(vec_flat)
[1] FALSE
> 
> decreasing(vec_inc)
[1] FALSE
> decreasing(vec_dec)
[1] TRUE
> decreasing(vec_ran)
[1] FALSE
> decreasing(vec_flat)
[1] FALSE
> 
> unvarying(vec_inc)
[1] FALSE
> unvarying(vec_dec)
[1] FALSE
> unvarying(vec_ran)
[1] FALSE
> unvarying(vec_flat)
[1] TRUE
> 
> library(ggplot2)
> library(gghighlight)
Error in library(gghighlight) : there is no package called ‘gghighlight’
Execution halted
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘broom.mixed’

Package suggested but not available for checking: ‘lme4’

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

Packages suggested but not available for checking:
  'brms', 'broom.mixed', 'cmprsk', 'gam', 'glmmTMB', 'gtsummary',
  'lfe', 'lme4', 'plm', 'rstanarm', 'survey', 'tidycmprsk'

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

Packages suggested but not available for checking:
  'brms', 'dotwhisker', 'gamlss', 'glmmADMB', 'glmmTMB', 'lmerTest',
  'lme4', 'MCMCglmm', 'pbkrtest', 'rstan', 'rstanarm', 'R2jags'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'AER', 'betareg', 'biglm', 'btergm', 'car', 'caret', 'cmprsk', 'drc',
  'epiR', 'ergm', 'gam', 'glmnet', 'glmnetUtils', 'gmm', 'Hmisc',
  'irlba', 'joineRML', 'ks', 'lfe', 'lme4', 'lmtest', 'lsmeans',
  'maptools', 'mediation', 'metafor', 'mfx', 'mlogit', 'multcomp',
  'orcutt', 'plm', 'poLCA', 'quantreg', 'rgeos', 'robust', 'rsample',
  'spdep', 'spatialreg', 'speedglm', 'survey', 'systemfit', 'tseries',
  'vars'
Running examples in ‘broom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tidy.btergm
> ### Title: Tidy a(n) btergm object
> ### Aliases: tidy.btergm btergm_tidiers
> 
> ### ** Examples
> 
> 
> # feel free to ignore the following line—it allows {broom} to supply 
> # examples without requiring the model-supplying package to be installed.
> if (requireNamespace("bbmle", quietly = TRUE)) {
+   if (requireNamespace("network", quietly = TRUE)) {
+ 
+ library(btergm)
+ library(network)
+ 
+ set.seed(5)
+ 
+ # create 10 random networks with 10 actors
+ networks <- list()
+ for (i in 1:10) {              
+   mat <- matrix(rbinom(100, 1, .25), nrow = 10, ncol = 10)
+   diag(mat) <- 0              
+   nw <- network(mat)  
+   networks[[i]] <- nw         
+ }
+ 
+ # create 10 matrices as covariates
+ covariates <- list()
+ for (i in 1:10) {              
+   mat <- matrix(rnorm(100), nrow = 10, ncol = 10)
+   covariates[[i]] <- mat
+ }
+ 
+ # fit the model
+ mod <- btergm(networks ~ edges + istar(2) + edgecov(covariates), R = 100)
+ 
+ # summarize model fit with tidiers
+ tidy(mod)
+ 
+   }
+ }
Error in library(btergm) : there is no package called ‘btergm’
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 ‘benchmarks.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘benchmarks.Rmd’ using ‘UTF-8’... failed to complete the test
Packages required but not available: 'taxize', '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’
Packages required but not available: 'afex', 'lmerTest', 'mediation'

Packages suggested but not available for checking:
  'rio', 'haven', 'car', 'phia', 'lmtest', 'lme4', 'vars',
  'BayesFactor', 'GGally'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Package required but not available: ‘torch’

Package suggested but not available for checking: ‘recipes’

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

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

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

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

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

Packages suggested but not available for checking:
  'surveillance', 'spdep', '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/BSDA.Rcheck/00install.out’ for details.
Packages required but not available: 'viridis', 'rstan', 'DiagrammeR'

Packages suggested but not available for checking:
  'devtools', 'ggfortify', 'plotly', 'visdat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BSGS.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: ‘Epi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mefa4’

Package suggested but not available for checking: ‘detect’

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

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

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

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

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

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

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

--- re-building ‘sde_model.Rmd’ using rmarkdown
Quitting from lines 52-62 (sde_model.Rmd) 
Error: processing vignette ‘sde_model.Rmd’ failed with diagnostics:
there is no package called 'sde'
--- failed re-building ‘sde_model.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'sn', 'ssmn', 'ClusterR'

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/bsTools.Rcheck/00install.out’ for details.
Package required but not available: ‘doParallel’

Packages suggested but not available for checking: 'hdi', '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: 'BoomSpikeSlab', 'xts', 'Boom'

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

Packages suggested but not available for checking: 'fastglm', 'Bergm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gvcm.cat’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BTLLasso.Rcheck/00install.out’ for details.
Packages required but not available: 'ggforce', 'R2jags'

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: ‘BTYD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BTYD.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: ‘Amelia’

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: ‘openair’
Running examples in ‘buffeRs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: buffer_windrose
> ### Title: A wind-rose shaped buffer function
> ### Aliases: buffer_windrose
> ### Keywords: Wind-rose wind
> 
> ### ** Examples
> 
> example_point = sf::st_point(c(1,2))
> example_point = sf::st_sfc(example_point)
> example_point = sf::st_sf(example_point)
> 
> openair::windRose(wind_sample) -> wind_sample_wind_rose
Error in loadNamespace(x) : there is no package called ‘openair’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘buffeRs.Rmd’ using rmarkdown
Quitting from lines 42-43 (buffeRs.Rmd) 
Error: processing vignette ‘buffeRs.Rmd’ failed with diagnostics:
there is no package called 'openair'
--- failed re-building ‘buffeRs.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘lme4’

Packages suggested but not available for checking:
  'gamm4', 'glmertree', 'glmmTMB', 'lmerTest', 'partykit', 'pbkrtest'

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:
  'mda', 'mpath', 'mboost', 'earth', 'elasticnet', 'rms', 'bst'

Packages suggested but not available for checking: 'TH.data', '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:
  'gprofiler2', 'edgeR', 'DESeq2', 'ggrepel', 'ComplexHeatmap',
  'ggforce', 'noisyr', 'ggrastr'

Packages suggested but not available for checking:
  'AnnotationDbi', 'org.Hs.eg.db', 'org.Mm.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/bulletcp.Rcheck/00install.out’ for details.
Packages required but not available: 'plotly', 'smoother'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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: 'car', 'rsq'
Error(s) in re-building vignettes:
  ...
--- re-building ‘bumbl.Rmd’ using rmarkdown
Quitting from lines 19-21 (bumbl.Rmd) 
Error: processing vignette ‘bumbl.Rmd’ failed with diagnostics:
there is no package called 'car'
--- failed re-building ‘bumbl.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bunching.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
plot.bursts: no visible global function definition for ‘axis’
plot.bursts: no visible global function definition for ‘arrows’
Undefined global functions or variables:
  arrows axis
Consider adding
  importFrom("graphics", "arrows", "axis")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'C50', 'caret', 'ddalpha', 'dimRed', 'earth', 'flexsurv', 'ipred',
  'mda', 'NMF', 'recipes', 'rsample', 'TH.data'
Running examples in ‘butcher-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: axe-C5.0
> ### Title: Axing a C5.0.
> ### Aliases: axe-C5.0 axe_call.C5.0 axe_ctrl.C5.0 axe_fitted.C5.0
> 
> ### ** Examples
> 
> # Load libraries
> suppressWarnings(suppressMessages(library(parsnip)))
> suppressWarnings(suppressMessages(library(rsample)))
Error in library(rsample) : there is no package called ‘rsample’
Execution halted
Packages required but not available:
  'doParallel', 'lava', 'prodlim', 'riskRegression'

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: ‘vars’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bvartools.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BVARverse.Rcheck/00install.out’ for details.
Rd file 'bvenn.Rd':
  \examples lines wider than 100 characters:
                     bvenn(list(Set1 = sample(letters, 16), Set2 = sample(letters, 3+ 3*j), Set3 = sample(letters, 7)), add = TRUE, fontsize ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Malformed Description field: should contain one or more complete sentences.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bvpSolve.Rcheck/00install.out’ for details.
Package required but not available: ‘doParallel’

Package suggested but not available for checking: ‘doMPI’

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

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: ‘crossdes’

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:
  'glmnet', 'tgp', 'peperr', 'penalizedSVM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/c212.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/c3net.Rcheck/00install.out’ for details.
Package required but not available: ‘viridis’

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

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

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

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

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

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

Package suggested but not available for checking: ‘gamm4’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'smoof', 'car'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘Adapting_Algorithm_for_CAISEr.Rmd’ using rmarkdown
Quitting from lines 51-73 (Adapting_Algorithm_for_CAISEr.Rmd) 
Error: processing vignette ‘Adapting_Algorithm_for_CAISEr.Rmd’ failed with diagnostics:
there is no package called 'smoof'
--- failed re-building ‘Adapting_Algorithm_for_CAISEr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'taxize', 'dendextend', 'heatmaply', 'plotly'

Packages suggested but not available for checking:
  'AnnotationDbi', 'KEGGREST', 'GO.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'wavethresh', 'LS2W'

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

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

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

Package suggested but not available for checking: ‘ReGenesees’

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 required but not available: 'fitdistrplus', '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/CallEshotgun.Rcheck/00install.out’ for details.
Packages required but not available:
  'R.utils', 'aroma.core', 'R.oo', 'R.filesets'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CAMAN.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'VAM', 'Seurat', 'edgeR', 'org.Hs.eg.db', 'org.Mm.eg.db',
  'AnnotationDbi'

Package suggested but not available for checking: ‘sctransform’

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’

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: ‘diagram’

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

Packages suggested but not available for checking:
  'raster', 'rgdal', 'taxize', 'unmarked', 'RSQLite'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'GenomicRanges', 'IRanges', 'S4Vectors'
Package unavailable to check Rd xrefs: ‘GenomicRanges’
Packages required but not available: 'car', 'heplots'

Package suggested but not available for checking: ‘rpart.plot’

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/canprot.Rcheck/00install.out’ for details.
Package required but not available: ‘Hmisc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘readr’
Packages required but not available:
  'doParallel', 'propagate', 'qtl2', 'qtl2convert'

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

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/cap.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/capushe.Rcheck/00install.out’ for details.
bootstrapCapwire: no visible global function definition for ‘quantile’
drawCapRatesBeta : <anonymous>: no visible global function definition
  for ‘rbeta’
drawCapRatesExp : <anonymous>: no visible global function definition
  for ‘rexp’
drawCapRatesGamma : <anonymous>: no visible global function definition
  for ‘rgamma’
drawCapRatesGeom : <anonymous>: no visible global function definition
  for ‘rgeom’
drawCapRatesUnif : <anonymous>: no visible global function definition
  for ‘runif’
partitionCountData : find.3.way.partitions: no visible global function
  definition for ‘dmultinom’
Undefined global functions or variables:
  dmultinom quantile rbeta rexp rgamma rgeom runif
Consider adding
  importFrom("stats", "dmultinom", "quantile", "rbeta", "rexp", "rgamma",
             "rgeom", "runif")
to your NAMESPACE file.
Package required but not available: ‘geometry’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'CARBayesdata', 'GGally', 'leaflet', 'MCMCpack', 'rgdal', 'spdep'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'CARBayesdata', 'GGally', 'leaflet', 'MCMCpack', 'rgdal', 'spdep',
  'truncdist'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Sub.pair: no visible global function definition for ‘qnorm’
as.record: no visible global function definition for ‘capture.output’
estN: no visible global function definition for ‘sd’
estN: no visible global function definition for ‘qnorm’
estN.bootstrap: no visible global function definition for ‘runif’
Undefined global functions or variables:
  capture.output qnorm runif sd
Consider adding
  importFrom("stats", "qnorm", "runif", "sd")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘sda’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/care.Rcheck/00install.out’ for details.
Package required but not available: ‘caret’

Packages suggested but not available for checking:
  'glmnet', 'ipred', 'klaR'

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

Package suggested but not available for checking: ‘Cubist’

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

Packages suggested but not available for checking:
  'BradleyTerry2', 'Cubist', 'earth', 'gam', 'ipred', 'klaR', 'mda',
  'pamr', 'party', 'themis'

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.
barplotEQR: no visible global function definition for ‘barplot’
barplotEQR: no visible global function definition for ‘abline’
barplotEQR: no visible global function definition for ‘par’
barplotEQR: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline barplot par text
Consider adding
  importFrom("graphics", "abline", "barplot", "par", "text")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘quantreg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RSQLite’
‘library’ or ‘require’ calls in package code:
  ‘MASS’ ‘RSQLite’ ‘grid’ ‘sm’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Running examples in ‘caroline-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bestBy
> ### Title: Find the "best" record within subgroups of a dataframe.
> ### Aliases: bestBy
> 
> ### ** Examples
> 
> 
> blast.results <- data.frame(score=c(1,2,34,4,5,3,23), 
+                             query=c('z','x','y','z','x','y','z'), 
+                             target=c('a','b','c','d','e','f','g')
+                             )
> best.hits.R <- bestBy(blast.results, by='query', best='score', inverse=TRUE)
> best.hits.R
  score query target
y    34     y      c
z    23     z      g
x     5     x      e
> ## or using SQLite
> best.hits.sql <- bestBy(blast.results, by='query', best='score', inverse=TRUE, sql=TRUE)
Loading required package: RSQLite
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘RSQLite’
Error in dbConnect(dbDriver("SQLite"), dbname = tmpfile) : 
  could not find function "dbConnect"
Calls: bestBy
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'VennDiagram', 'DESeq2', 'biomaRt', 'seqinr', 'xlsx'

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

Packages suggested but not available for checking:
  'alr4', 'coxme', 'effects', 'lmtest', 'rio', 'survey'

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: ‘np’

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

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

Package suggested but not available for checking: ‘cartography’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cartogram_cont
> ### Title: Calculate Contiguous Cartogram Boundaries
> ### Aliases: cartogram_cont cartogram_cont.SpatialPolygonsDataFrame
> ###   cartogram_cont.sf
> 
> ### ** Examples
> 
> 
> library(maptools)
Error in library(maptools) : there is no package called ‘maptools’
Execution halted
Packages required but not available: 'raster', 'rgeos', 'slippymath'

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

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

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

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

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: ‘fitdistrplus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘glmnet’
Packages required but not available: 'haven', 'labelled', 'survey', 'srvyr'

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: 'bipartite', '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/castor.Rcheck/00install.out’ for details.
Package required but not available: ‘caret’

Packages suggested but not available for checking:
  'doParallel', 'raster', 'mapview', 'latticeExtra', 'virtualspecies',
  'viridis', 'rgeos', 'stars', 'scam'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘caret’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ggspatial', 'raster', 'slippymath'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'rms', 'mlogit', 'Ecdat', 'party', 'lme4', 'vcdExtra', 'glmnet',
  'mboost', 'flexmix', 'GAMBoost', 'penalized'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/catdata.Rcheck/00install.out’ for details.
Package required but not available: ‘Rglpk’

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: ‘tidyverse’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
MDR.high.forward1: no visible global function definition for ‘combn’
MDR.sing.mod1: no visible global function definition for ‘combn’
MDR.sing.mod1: no visible global function definition for
  ‘complete.cases’
MDR.sing.mod1: no visible global function definition for ‘lm’
MDR.sing.mod1: no visible global function definition for ‘aov’
MDR.sing.mod1: no visible global function definition for ‘anova’
MDR.stage.forward1: no visible global function definition for ‘combn’
MDR.stage.forward1: no visible global function definition for
  ‘complete.cases’
MDR.stage.forward1: no visible global function definition for ‘lm’
MDR.stage.forward1: no visible global function definition for ‘resid’
MDR.stage.forward1: no visible global function definition for ‘pf’
MDR_forward1: no visible global function definition for
  ‘complete.cases’
MDR_forward1: no visible global function definition for ‘lm’
MDR_forward1: no visible global function definition for ‘aov’
low.anova: no visible global function definition for ‘complete.cases’
low.anova: no visible global function definition for ‘lm’
sing.mod1: no visible global function definition for ‘combn’
sing.mod1: no visible global function definition for ‘complete.cases’
sing.mod1: no visible global function definition for ‘lm’
sing.mod1: no visible global function definition for ‘pf’
Undefined global functions or variables:
  anova aov combn complete.cases lm pf resid
Consider adding
  importFrom("stats", "anova", "aov", "complete.cases", "lm", "pf",
             "resid")
  importFrom("utils", "combn")
to your NAMESPACE file.
Packages required but not available: 'DescTools', 'Hmisc'

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

Packages suggested but not available for checking:
  'entropart', 'fBasics', 'picante'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'irtoys', 'ltm'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/catIrt.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: 'plotly', 'tidyverse'

Package suggested but not available for checking: ‘viridis’

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

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.
Malformed Description field: should contain one or more complete sentences.
mi.inference: no visible binding for global variable ‘var’
mi.inference: no visible global function definition for ‘qt’
mi.inference: no visible global function definition for ‘pt’
Undefined global functions or variables:
  pt qt var
Consider adding
  importFrom("stats", "pt", "qt", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mlogit’
Malformed Description field: should contain one or more complete sentences.
ctab: no visible global function definition for ‘xtabs’
mob.eqmain: no visible global function definition for ‘model.matrix’
mob.qi: no visible global function definition for ‘C’
mob.qi: no visible binding for global variable ‘contr.treatment’
mob.rc1: no visible global function definition for ‘C’
mob.rc1: no visible binding for global variable ‘contr.treatment’
mob.rc1: no visible global function definition for ‘model.matrix’
mob.symint: no visible global function definition for ‘model.matrix’
print.ctab: no visible global function definition for ‘ftable’
Undefined global functions or variables:
  C contr.treatment ftable model.matrix xtabs
Consider adding
  importFrom("stats", "C", "contr.treatment", "ftable", "model.matrix",
             "xtabs")
to your NAMESPACE file.
Rd file 'ctab.Rd':
  \usage lines wider than 90 characters:
     ctab(...,dec.places=NULL,digits=NULL,type=NULL,style=NULL,row.vars=NULL,col.vars=NULL,percentages=NULL,addmargins=NULL)

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

These lines will be truncated in the PDF manual.
Packages required but not available: 'caret', 'farff'

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.
Package required but not available: ‘ltm’

Package suggested but not available for checking: ‘catIrt’

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: ‘DiagrammeR’

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

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

Package suggested but not available for checking: ‘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’
Package required but not available: ‘gam’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fda', 'cvTools', '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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/causaloptim.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'CBPS', 'rstan'
Packages required but not available: 'forestplot', 'ggdag'

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

Package suggested but not available for checking: ‘DeclareDesign’

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

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

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

Packages suggested but not available for checking:
  'missForest', 'knockoff', 'caret', 'bartMachine', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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: ‘rstan’

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 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/ccaPP.Rcheck/00install.out’ for details.
Packages required but not available: 'fda', 'fields'

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

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

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/cccd.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ccChooser.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ccda.Rcheck/00install.out’ for details.
Packages required but not available: 'doParallel', 'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘graph’
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/cchs.Rcheck/00install.out’ for details.
Packages required but not available: 'hdbinseg', 'GeneNet'

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

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

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

Package suggested but not available for checking: ‘nnTensor’

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

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

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: ‘ddpcr’

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

Package suggested but not available for checking: ‘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/cdb.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: ‘ks’

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.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘raster’

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

Packages which this enhances but not available for checking:
  'dina', 'GDINA', 'mirt', 'rrum', 'TAM'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CDM.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘tfplot’
Running examples in ‘CDNmoney-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CanadianCreditData
> ### Title: Canadian Credit Aggregates
> ### Aliases: CanadianCreditData CanadianCreditData.asof.6Mar2009
> ###   CanadianCreditData.asof.5Jun2007 CanadianCreditData.asof.3Mar2006
> ###   CanadianCreditData.asof.28Jan2005 TotalCredit ConsumerCredit
> ###   ResidentialMortgage ShortTermBusinessCredit OtherBusinessCredit
> ### Keywords: datasets
> 
> ### ** Examples
> 
>  require("tframe")
Loading required package: tframe
>  require("tfplot")
Loading required package: tfplot
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘tfplot’
>  data("CanadianCreditData", package="CDNmoney")
> 
>  tfplot(TotalCredit, ConsumerCredit, ResidentialMortgage,
+     ShortTermBusinessCredit, OtherBusinessCredit) 
Error in tfplot(TotalCredit, ConsumerCredit, ResidentialMortgage, ShortTermBusinessCredit,  : 
  could not find function "tfplot"
Execution halted
Package suggested but not available for checking: ‘eemR’
Packages required but not available: 'plotly', 'freqparcoord', 'partools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘out.png’ ‘out1.txt’ ‘out2.txt’
Package required but not available: ‘mixtools’

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: 'graph', '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/celestial.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'fractaldim', 'wordspace', 'uwot', 'dendextend', 'ggbeeswarm'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cellVolumeDist.Rcheck/00install.out’ for details.
Package required but not available: ‘rrcov’

Packages suggested but not available for checking:
  'robustHD', 'rospca', 'GSE'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', '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/cenGAM.Rcheck/00install.out’ for details.
Package required but not available: ‘tidycensus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mixsmsn’
'LazyData' is specified without a 'data' directory
cenNID: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Package required but not available: ‘duckdb’

Package suggested but not available for checking: ‘chilemapas’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/censorcopula.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
MomNIT: no visible global function definition for ‘dnorm’
MomNIT: no visible global function definition for ‘pnorm’
cdfNI: no visible global function definition for ‘pnorm’
cdfNI: no visible global function definition for ‘pt’
em.cens: no visible global function definition for ‘lm’
em.cens: no visible global function definition for ‘coefficients’
em.cens : ft: no visible global function definition for ‘dt’
em.cens : ft: no visible global function definition for ‘pt’
em.cens: no visible global function definition for ‘optimize’
em.cens: no visible global function definition for ‘dnorm’
em.cens: no visible global function definition for ‘pnorm’
em.cens: no visible global function definition for ‘sd’
Undefined global functions or variables:
  coefficients dnorm dt lm optimize pnorm pt sd
Consider adding
  importFrom("stats", "coefficients", "dnorm", "dt", "lm", "optimize",
             "pnorm", "pt", "sd")
to your NAMESPACE file.
Packages required but not available: 'maxLik', 'plm'

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

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

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

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 ‘Census2016.Rmd’ using rmarkdown
Quitting from lines 63-74 (Census2016.Rmd) 
Error: processing vignette ‘Census2016.Rmd’ failed with diagnostics:
object ‘.CensusDataTables’ not found
--- failed re-building ‘Census2016.Rmd’

SUMMARY: processing the following file failed:
  ‘Census2016.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/censusr.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'expm', 'linkcomm'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/centiserve.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/centralplot.Rcheck/00install.out’ for details.
Packages required but not available: 'msm', 'sna'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gravity’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CepLDA.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
Packages required but not available: 'slippymath', 'raster', 'spex'

Package suggested but not available for checking: ‘rgdal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rrcov', 'robust', 'alr3'
select_lambda: no visible global function definition for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘plotly’

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: 'haven', 'readr', '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/ceterisParibus.Rcheck/00install.out’ for details.
Package required but not available: ‘Hmisc’

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

Packages suggested but not available for checking: 'ggrepel', 'RSQLite'

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

Packages suggested but not available for checking:
  'BSGW', 'BayesMixSurv', 'Hmisc', 'randomForestSRC'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
cf_estimate_quantiles: no visible global function definition for
  ‘qnorm’
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
Packages required but not available: 'rgdal', 'raster', 'doParallel'

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.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘GLAD’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cghRA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cglasso.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
Package required but not available: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'BayesFactor', 'DescTools', 'ggmosaic', 'ggrepel', 'partykit',
  'sjstats'

Package suggested but not available for checking: ‘BSDA’

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

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

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

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

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

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

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

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

Package suggested but not available for checking: ‘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/changepointsVar.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: ‘devtools’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Hartree2Joule: no visible binding for global variable
  ‘universalConstants’
Hertz2Joule: no visible binding for global variable
  ‘universalConstants’
Joule2Hartree: no visible binding for global variable
  ‘universalConstants’
Joule2Hertz: no visible binding for global variable
  ‘universalConstants’
Joule2Kelvin: no visible binding for global variable
  ‘universalConstants’
Joule2centimeterMinusOne: no visible binding for global variable
  ‘universalConstants’
Joule2electronVolt: no visible binding for global variable
  ‘universalConstants’
Joule2kiloCaloriePerMole: no visible binding for global variable
  ‘universalConstants’
Joule2kiloJoulePerMole: no visible binding for global variable
  ‘universalConstants’
KMC: no visible global function definition for ‘runif’
Kelvin2Joule: no visible binding for global variable
  ‘universalConstants’
LandauZener: no visible binding for global variable
  ‘universalConstants’
LandauZenerProbability: no visible binding for global variable
  ‘universalConstants’
Marcus: no visible binding for global variable ‘universalConstants’
MarcusLevichJortner: no visible binding for global variable
  ‘universalConstants’
centimeterMinusOne2Joule: no visible binding for global variable
  ‘universalConstants’
electronVolt2Joule: no visible binding for global variable
  ‘universalConstants’
kiloCaloriePerMole2Joule: no visible binding for global variable
  ‘universalConstants’
kiloJoulePerMole2Joule: no visible binding for global variable
  ‘universalConstants’
Undefined global functions or variables:
  runif universalConstants
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CHCN.Rcheck/00install.out’ for details.
Package required but not available: ‘geometry’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Rd file 'chebR.Rd':
  \examples lines wider than 100 characters:
     return(list(coefs=rlist$xx[1:n],resids=rlist$bb[1:m],rank=rlist$rank,iter=rlist$iter,ocode=rlist$ocode))

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘devtools’
Package suggested but not available for checking: ‘darts’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'spinifex', 'plotly'

Packages suggested but not available for checking: 'lightgbm', 'gganimate'

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

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

Packages suggested but not available for checking:
  'irlba', 'multiway', 'R.utils', 'mlrMBO', 'smoof', 'mlr', 'CMLS'

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

Packages suggested but not available for checking:
  'R.utils', 'seriation', 'gsubfn', 'speaq', 'elasticnet', 'irlba',
  'chemometrics', 'hyperSpec'

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

Packages suggested but not available for checking:
  'ChemoSpec', 'ChemoSpec2D', 'irlba', 'multiway', 'roxut'

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

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

Packages suggested but not available for checking:
  'GenomicInteractions', 'GenomicRanges', 'Gviz', 'countreg'

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘chillR’
Packages required but not available:
  'fields', 'metR', 'R.utils', 'raster', 'RMAWGEN'

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

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

Package suggested but not available for checking: ‘car’

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

Packages suggested but not available for checking: 'drc', 'qpcR'

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

Package suggested but not available for checking: ‘cmdstanr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘coin’
Malformed Description field: should contain one or more complete sentences.
Qh.times.dhyper: no visible global function definition for ‘var’
Qh.times.dhyper: no visible global function definition for ‘pnorm’
Qh.times.dhyper: no visible global function definition for ‘dhyper’
TDiM: no visible global function definition for ‘sd’
choplump.default: no visible global function definition for
  ‘flush.console’
choplump.formula: no visible global function definition for ‘terms’
cm.compact: no visible global function definition for ‘dhyper’
Undefined global functions or variables:
  dhyper flush.console pnorm sd terms var
Consider adding
  importFrom("stats", "dhyper", "pnorm", "sd", "terms", "var")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘choplumpValidation.Rnw’ using Sweave

Error: processing vignette ‘choplumpValidation.Rnw’ failed with diagnostics:
 chunk 6 
Error in library(coin) : there is no package called ‘coin’

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

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'acs', 'Hmisc', 'ggmap', 'tigris', 'tidycensus'

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
Malformed Description field: should contain one or more complete sentences.
parse_counts: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Packages required but not available:
  'dygraphs', 'plotly', 'readr', 'viridis'

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 required but not available: ‘raster’

Package suggested but not available for checking: ‘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/CHsharp.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘RSQLite’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/chunked.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Biobase', 'ggraph'

Packages suggested but not available for checking:
  'clustree', 'ComplexHeatmap', 'plotly', '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/CICA.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'edgeR', 'Seurat', 'doParallel', 'viridis'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'sna', 'centiserve', 'FactoMineR', 'factoextra', 'GGally',
  'dendextend', 'viridis'

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

Packages suggested but not available for checking:
  'BSDA', 'userfriendlyscience'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'dendextend', 'ComplexHeatmap'
Unavailable namespace imported from by a ‘:::’ call: ‘ComplexHeatmap’
  See the note in ?`:::` about the use of this operator.
Running examples in ‘circlize-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: circos.dendrogram
> ### Title: Add circular dendrograms
> ### Aliases: circos.dendrogram
> 
> ### ** Examples
> 
> load(system.file(package = "circlize", "extdata", "bird.orders.RData"))
> 
> labels = hc$labels  # name of birds
> ct = cutree(hc, 6)  # cut tree into 6 pieces
> n = length(labels)  # number of bird species
> dend = as.dendrogram(hc)
> 
> circos.par(cell.padding = c(0, 0, 0, 0))
> circos.initialize(sectors = "a", xlim = c(0, n)) # only one sector
> max_height = attr(dend, "height")  # maximum height of the trees
> circos.trackPlotRegion(ylim = c(0, 1), bg.border = NA, track.height = 0.3,
+     panel.fun = function(x, y) {
+         for(i in seq_len(n)) {
+             circos.text(i-0.5, 0, labels[i], adj = c(0, 0.5),
+                 facing = "clockwise", niceFacing = TRUE,
+                 col = ct[labels[i]], cex = 0.7)
+         }
+ })
> 
> suppressPackageStartupMessages(require(dendextend))
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘dendextend’
> dend = color_branches(dend, k = 6, col = 1:6)
Error in color_branches(dend, k = 6, col = 1:6) : 
  could not find function "color_branches"
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘CircStats’

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

Package suggested but not available for checking: ‘plotly’

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

Package suggested but not available for checking: ‘ggrepel’

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

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

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 required but not available: ‘MESS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
cit.assignBcmst: no visible binding for global variable ‘citbcmst’
cit.assignBcmst : <anonymous>: no visible global function definition
  for ‘median’
cit.assignBcmst: no visible global function definition for ‘prcomp’
cit.assignBcmst: no visible global function definition for ‘par’
cit.assignBcmst: no visible global function definition for ‘lines’
cit.assignBcmst: no visible global function definition for ‘legend’
cit.centroids : <anonymous>: no visible global function definition for
  ‘median’
cit.centroids : <anonymous>: no visible global function definition for
  ‘var’
cit.dist: no visible global function definition for ‘dist’
cit.dist: no visible global function definition for ‘as.dist’
cit.dist: no visible global function definition for ‘cor’
cit.distToCentroids: no visible global function definition for
  ‘quantile’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘median’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘mad’
Undefined global functions or variables:
  as.dist citbcmst cor dist legend lines mad median par prcomp quantile
  var
Consider adding
  importFrom("graphics", "legend", "lines", "par")
  importFrom("stats", "as.dist", "cor", "dist", "mad", "median",
             "prcomp", "quantile", "var")
to your NAMESPACE file.
cit.assignCcmst: no visible binding for global variable ‘citccmst’
cit.assignCcmst : <anonymous>: no visible global function definition
  for ‘median’
cit.assignCcmst : median.na: no visible global function definition for
  ‘median’
cit.assignCcmst: no visible global function definition for ‘prcomp’
cit.assignCcmst: no visible global function definition for ‘par’
cit.assignCcmst: no visible global function definition for ‘lines’
cit.assignCcmst: no visible global function definition for ‘legend’
cit.centroids : <anonymous>: no visible global function definition for
  ‘median’
cit.centroids : <anonymous>: no visible global function definition for
  ‘var’
cit.dist: no visible global function definition for ‘dist’
cit.dist: no visible global function definition for ‘as.dist’
cit.dist: no visible global function definition for ‘cor’
cit.distToCentroids: no visible global function definition for
  ‘quantile’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘median’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘mad’
Undefined global functions or variables:
  as.dist citccmst cor dist legend lines mad median par prcomp quantile
  var
Consider adding
  importFrom("graphics", "legend", "lines", "par")
  importFrom("stats", "as.dist", "cor", "dist", "mad", "median",
             "prcomp", "quantile", "var")
to your NAMESPACE file.
Packages required but not available: 'arm', 'lme4'

Package suggested but not available for checking: ‘SPREDA’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
CityPlot: no visible global function definition for ‘read.table’
CityPlot: no visible global function definition for ‘tail’
CityPlot: no visible global function definition for ‘pdf’
CityPlot: no visible global function definition for ‘split.screen’
CityPlot: no visible global function definition for ‘screen’
CityPlot: no visible global function definition for ‘par’
CityPlot: no visible global function definition for ‘rect’
CityPlot: no visible global function definition for ‘text’
CityPlot: no visible global function definition for ‘lines’
CityPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off lines par pdf read.table rect screen split.screen tail text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "rect", "screen",
             "split.screen", "text")
  importFrom("utils", "read.table", "tail")
to your NAMESPACE file.
Packages required but not available:
  'dataRetrieval', 'EcoHydRology', 'tgp', 'xts'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ciu.meta.explain
> ### Title: ciu.meta.explain
> ### Aliases: ciu.meta.explain
> 
> ### ** Examples
> 
> # Explaining the classification of an Iris instance with lda model.
> # We use a versicolor (instance 100).
> library(MASS)
> test.ind <- 100
> iris_test <- iris[test.ind, 1:4]
> iris_train <- iris[-test.ind, 1:4]
> iris_lab <- iris[[5]][-test.ind]
> model <- lda(iris_train, iris_lab)
> 
> # Create CIU object
> ciu <- ciu.new(model, Species~., iris)
> 
> # Get ciu.meta.result. This can either be 'ciu$meta.explain(...)'
> # or 'ciu.meta.explain(ciu, ...)'
> ciu.meta <- ciu$meta.explain(iris_test)
> 
> # Use same result for different visualisations.
> ciu$ggplot.col.ciu(ciu.meta = ciu.meta)
> ciu$barplot.ciu(ind.output = 2, ciu.meta = ciu.meta)
> ciu$pie.ciu(ind.output = 2, ciu.meta = ciu.meta)
> 
> # Same with Boston Housing data set.
> library(caret)
Error in library(caret) : there is no package called ‘caret’
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘desciption-ciuupi.Rmd’
Package suggested but not available for checking: ‘R.utils’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘jose’

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

Package suggested but not available for checking: ‘cregg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lmtest', '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/ckanr.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggforce', 'ggraph', 'readr', 'vroom'

Package suggested but not available for checking: ‘tidyverse’

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

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: ‘stepR’

Packages suggested but not available for checking: 'R.cache', '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/clam.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'fGarch', 'FRAPO'
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Biobase’

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 required but not available: 'graph', 'Rgraphviz'

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 suggested but not available for checking: ‘rggobi’
‘library’ or ‘require’ call to ‘rggobi’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
generate_data : <anonymous>: no visible global function definition for
  ‘runif’
knnf: no visible global function definition for ‘terms’
rescaler.default: no visible global function definition for ‘sd’
rescaler.default: no visible global function definition for ‘median’
rescaler.default: no visible global function definition for ‘mad’
simvar.numeric: no visible global function definition for ‘runif’
Undefined global functions or variables:
  mad median runif sd terms
Consider adding
  importFrom("stats", "mad", "median", "runif", "sd", "terms")
to your NAMESPACE file.
Package suggested but not available for checking: ‘spData’
Error(s) in re-building vignettes:
  ...
--- re-building ‘headtailsR.Rmd’ using rmarkdown
Quitting from lines 250-252 (headtailsR.Rmd) 
Error: processing vignette ‘headtailsR.Rmd’ failed with diagnostics:
there is no package called 'spData'
--- failed re-building ‘headtailsR.Rmd’

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

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

Packages suggested but not available for checking:
  'rpart.plot', 'robCompositions'

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: ‘readtext’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Biostrings’

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 vignette with placeholder title ‘Vignette Title’:
  ‘my-vignette.Rmd’
Packages required but not available: 'rgeos', 'maptools'

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

Package suggested but not available for checking: ‘timetk’

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

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.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘arrow’

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

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

Packages suggested but not available for checking: 'onion', 'lorentz'

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

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

Packages suggested but not available for checking: 'climatol', 'gganimate'

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

Package suggested but not available for checking: ‘rangeBuilder’

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

Packages suggested but not available for checking:
  'fields', 'gstat', 'raster'

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

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

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

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: 'clinUtils', 'haven', 'plotly'

Packages suggested but not available for checking:
  'inTextSummaryTable', 'patientProfilesVis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'DoseFinding', '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
'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.
gxe.cc: no visible global function definition for ‘qnorm’
gxe.coh: no visible global function definition for ‘qnorm’
utility.cc: no visible global function definition for ‘qnorm’
utility.coh: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
Package required but not available: ‘haven’

Package suggested but not available for checking: ‘plotly’

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.
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/clogitL1.Rcheck/00install.out’ for details.
Package required but not available: ‘quantmod’

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

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/cloudml.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘httptest’
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(cloudos)
  
  Welcome to Lifebit's CloudOS R client 
  For Documentation visit - https://lifebit-ai.github.io/cloudos/ 
  This package is under active development. If you found any issues, 
  Please reach out here - https://github.com/lifebit-ai/cloudos/issues 
  
  > 
  > Sys.setenv(CLOUDOS_BASEURL = "api")
  > Sys.setenv(CLOUDOS_TEAMID = "5f7c8696d6ea46288645a89f")
  > Sys.setenv(CLOUDOS_TOKEN = "no real")
  > 
  > test_check("cloudos")
  Error in library(httptest) : there is no package called 'httptest'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Package required but not available: ‘rio’

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:
  'metafor', 'mlmRev', 'AER', 'plm', 'lme4'
Running examples in ‘clubSandwich-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coef_test
> ### Title: Test all or selected regression coefficients in a fitted model
> ### Aliases: coef_test
> 
> ### ** Examples
> 
> data("Produc", package = "plm")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘plm’
Calls: data -> find.package
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Wald-tests-in-clubSandwich.Rmd’ using rmarkdown
Registered S3 method overwritten by 'clubSandwich':
  method    from    
  bread.mlm sandwich
Quitting from lines 22-32 (Wald-tests-in-clubSandwich.Rmd) 
Error: processing vignette ‘Wald-tests-in-clubSandwich.Rmd’ failed with diagnostics:
there is no package called 'AER'
--- failed re-building ‘Wald-tests-in-clubSandwich.Rmd’

--- re-building ‘meta-analysis-with-CRVE.Rmd’ using rmarkdown
Quitting from lines 69-77 (meta-analysis-with-CRVE.Rmd) 
Error: processing vignette ‘meta-analysis-with-CRVE.Rmd’ failed with diagnostics:
there is no package called 'metafor'
--- failed re-building ‘meta-analysis-with-CRVE.Rmd’

--- re-building ‘panel-data-CRVE.Rmd’ using rmarkdown
Quitting from lines 93-98 (panel-data-CRVE.Rmd) 
Error: processing vignette ‘panel-data-CRVE.Rmd’ failed with diagnostics:
there is no package called 'plm'
--- failed re-building ‘panel-data-CRVE.Rmd’

SUMMARY: processing the following files failed:
  ‘Wald-tests-in-clubSandwich.Rmd’ ‘meta-analysis-with-CRVE.Rmd’ ‘panel-data-CRVE.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages which this enhances but not available for checking:
  'cba', 'flexclust', 'flexmix'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ClueR.Rcheck/00install.out’ for details.
Package required but not available: ‘tableone’

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: 'ALDqr', 'quantreg'

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.
Packages required but not available: 'mcclust', 'fossil'

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

Packages suggested but not available for checking:
  'dendextend', 'Seurat', 'readr'

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

Package suggested but not available for checking: ‘ClustVarLV’

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

Packages suggested but not available for checking: 'condSURV', 'plotly'

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

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

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

Package suggested but not available for checking: ‘tidyverse’

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

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
Packages required but not available: 'car', 'clValid', 'dendextend'

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

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

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

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

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

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'msm', '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/ClustMMDD.Rcheck/00install.out’ for details.
Package required but not available: ‘BAMBI’

Package suggested but not available for checking: ‘tidyverse’

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.
Package required but not available: ‘MixSim’

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

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

Packages suggested but not available for checking:
  'SingleCellExperiment', 'Seurat', 'SummarizedExperiment'

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.
Package required but not available: ‘klaR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
braycurtis: no visible global function definition for ‘as.dist’
czekanowski: no visible global function definition for ‘as.dist’
findComplementaryIndices: no visible global function definition for
  ‘na.omit’
genSimilarityProfile: no visible global function definition for ‘dist’
simprof: no visible global function definition for ‘dist’
simprof: no visible global function definition for ‘hclust’
simprof.plot : <local> : colorizer: no visible global function
  definition for ‘is.leaf’
simprof.plot: no visible global function definition for ‘rainbow’
simprof.plot: no visible global function definition for ‘dendrapply’
simprof.plot: no visible global function definition for ‘as.dendrogram’
Undefined global functions or variables:
  as.dendrogram as.dist dendrapply dist hclust is.leaf na.omit rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "as.dendrogram", "as.dist", "dendrapply", "dist",
             "hclust", "is.leaf", "na.omit")
to your NAMESPACE file.
Package required but not available: ‘doParallel’

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

Package suggested but not available for checking: ‘doParallel’

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.
Packages suggested but not available for checking:
  'Biobase', 'annotate', 'GO.db', 'moe430a.db'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/clValid.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/clv.Rcheck/00install.out’ for details.
Package required but not available: ‘smoof’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
alpha.cronbach: no visible global function definition for ‘cov’
alpha.curve: no visible global function definition for ‘text’
Undefined global functions or variables:
  cov text
Consider adding
  importFrom("graphics", "text")
  importFrom("stats", "cov")
to your NAMESPACE file.
Packages required but not available: 'x3ptools', 'imager', 'quantreg'

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: 'glmnet', 'sparsenet'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CMF.from.model.matrices
> ### Title: Create a CMF model object from fitted matrices
> ### Aliases: CMF.from.model.matrices
> 
> ### ** Examples
> 
> ### Example 'adopting' a model from 'recosystem'
> library(cmfrec)
> library(recosystem)
> library(recommenderlab)
Error in library(recommenderlab) : 
  there is no package called ‘recommenderlab’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cmfrec_vignette.Rmd’ using rmarkdown
Quitting from lines 108-116 (cmfrec_vignette.Rmd) 
Error: processing vignette ‘cmfrec_vignette.Rmd’ failed with diagnostics:
there is no package called 'MatrixExtra'
--- failed re-building ‘cmfrec_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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/CMLS.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘twang’

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/cmprsk.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'tidyverse', 'ggpubr'
Running examples in ‘cmpsR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cmps_segment_plot
> ### Title: Plot the selected basis segment and its cross-correlation curve
> ###   at all scales based on the results of CMPS algorithm
> ### Aliases: cmps_segment_plot
> 
> ### ** Examples
> 
> library(tidyverse)
Error in library(tidyverse) : there is no package called ‘tidyverse’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cmpsR-vignette.Rmd’ using rmarkdown
Quitting from lines 11-25 (cmpsR-vignette.Rmd) 
Error: processing vignette ‘cmpsR-vignette.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘cmpsR-vignette.Rmd’

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

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

Packages suggested but not available for checking: 'cmsaf', 'cmsafvis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'cmsafops', 'cmsafvis', 'fields', 'mapproj', 'maptools', 'R.utils',
  'raster', 'rworldxtra'

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

Package suggested but not available for checking: ‘plotKML’

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: ‘readr’

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.
Packages suggested but not available for checking:
  'censReg', 'AER', 'maxLik'
Running examples in ‘cmtest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cmtest
> ### Title: Conditional moments test
> ### Aliases: cmtest cmtest.tobit cmtest.tobit1 cmtest.censReg cmtest.glm
> ### Keywords: htest
> 
> ### ** Examples
> 
> # replication of Wells (2003) and Pagan and Vella (1989) using Fair's data
> library("AER")
Error in library("AER") : there is no package called ‘AER’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cmtest.Rmd’ using rmarkdown
Quitting from lines 284-289 (cmtest.Rmd) 
Error: processing vignette ‘cmtest.Rmd’ failed with diagnostics:
there is no package called 'maxLik'
--- failed re-building ‘cmtest.Rmd’

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

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

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

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

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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'adlift', 'nlt'

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

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 required but not available: ‘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/CNprep.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rstan', 'vegan'

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

Packages suggested but not available for checking:
  'ComplexHeatmap', 'plotly', 'InteractionSet', 'GenomicRanges',
  'GenomicFeatures', 'IRanges', 'heatmaply', 'S4Vectors',
  'GenomeInfoDb', 'BSgenome.Hsapiens.UCSC.hg19'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'abc', 'phyclust'
Error(s) in re-building vignettes:
  ...
--- re-building ‘coala-abc.Rmd’ using rmarkdown
Quitting from lines 72-75 (coala-abc.Rmd) 
Error: processing vignette ‘coala-abc.Rmd’ failed with diagnostics:
there is no package called 'abc'
--- failed re-building ‘coala-abc.Rmd’

--- re-building ‘coala-data-import.Rmd’ using rmarkdown
--- finished re-building ‘coala-data-import.Rmd’

--- re-building ‘coala-examples.Rmd’ using rmarkdown
--- finished re-building ‘coala-examples.Rmd’

--- re-building ‘coala-extend.Rmd’ using rmarkdown
--- finished re-building ‘coala-extend.Rmd’

--- re-building ‘coala-install.Rmd’ using rmarkdown
--- finished re-building ‘coala-install.Rmd’

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

SUMMARY: processing the following file failed:
  ‘coala-abc.Rmd’

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

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 suggested but not available for checking:
  'twang', 'Matching', 'optmatch', 'CBPS', 'designmatch', 'MatchThem',
  'cem', 'mlogit'
Error(s) in re-building vignettes:
  ...
--- re-building ‘cobalt.Rmd’ using rmarkdown
 cobalt (Version 4.3.2, Build Date: 2022-01-19)

Attaching package: 'MatchIt'

The following object is masked _by_ '.GlobalEnv':

    lalonde

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

    lalonde

Quitting from lines 415-423 (cobalt.Rmd) 
Error: processing vignette ‘cobalt.Rmd’ failed with diagnostics:
Package 'mlogit' is needed for this function to work. Please install it.
--- failed re-building ‘cobalt.Rmd’

--- re-building ‘cobalt_A1_other_packages.Rmd’ using rmarkdown
##
## ebal Package: Implements Entropy Balancing.

## See http://www.stanford.edu/~jhain/ for additional information.


--- finished re-building ‘cobalt_A1_other_packages.Rmd’

--- re-building ‘cobalt_A2_segmented_data.Rmd’ using rmarkdown
--- finished re-building ‘cobalt_A2_segmented_data.Rmd’

--- re-building ‘cobalt_A3_longitudinal_treat.Rmd’ using rmarkdown
--- finished re-building ‘cobalt_A3_longitudinal_treat.Rmd’

--- re-building ‘cobalt_A4_love.plot.Rmd’ using rmarkdown
--- finished re-building ‘cobalt_A4_love.plot.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘snowfall’
‘library’ or ‘require’ calls in package code:
  ‘lars’ ‘randomForest’ ‘ridge’ ‘snowfall’ ‘tree’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
COBRA : COBRA.lars: no visible global function definition for ‘lars’
COBRA : COBRA.lars: no visible global function definition for
  ‘predict.lars’
COBRA : COBRA.tree: no visible global function definition for ‘tree’
COBRA : COBRA.tree: no visible global function definition for
  ‘as.formula’
COBRA : COBRA.tree: no visible global function definition for ‘predict’
COBRA : COBRA.ridge: no visible global function definition for
  ‘linearRidge’
COBRA : COBRA.ridge: no visible global function definition for
  ‘as.formula’
COBRA : COBRA.ridge: no visible global function definition for
  ‘predict’
COBRA : COBRA.randomForest: no visible global function definition for
  ‘randomForest’
COBRA : COBRA.randomForest: no visible global function definition for
  ‘predict’
COBRA: no visible global function definition for ‘sfInit’
COBRA: no visible global function definition for ‘sfLibrary’
COBRA: no visible global function definition for ‘sfExportAll’
COBRA: no visible global function definition for ‘sfSapply’
COBRA: no visible global function definition for ‘sfStop’
COBRA: no visible global function definition for ‘write.table’
COBRA: no visible global function definition for ‘pdf’
COBRA: no visible global function definition for ‘points’
COBRA: no visible global function definition for ‘legend’
COBRA: no visible global function definition for ‘abline’
COBRA: no visible global function definition for ‘lines’
COBRA: no visible global function definition for ‘dev.off’
COBRA: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  abline as.formula dev.new dev.off lars legend linearRidge lines pdf
  points predict predict.lars randomForest sfExportAll sfInit sfLibrary
  sfSapply sfStop tree write.table
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("graphics", "abline", "legend", "lines", "points")
  importFrom("stats", "as.formula", "predict")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Package required but not available: ‘quantreg’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘rkward’
Packages required but not available: 'glmnet', 'ggpubr'

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

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

Packages suggested but not available for checking:
  'lme4', 'rio', 'ufs', 'userfriendlyscience'

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

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

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

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
Error(s) in re-building vignettes:
  ...
--- re-building ‘codingMatrices.Rnw’ using knitr
Quitting from lines 1034-1035 (codingMatrices.Rnw) 
Error: processing vignette ‘codingMatrices.Rnw’ failed with diagnostics:
there is no package called 'car'
--- failed re-building ‘codingMatrices.Rnw’

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

Error: Vignette re-building failed.
Execution halted
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: ‘rsem’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/coenoflex.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Rd file 'fast.flexsim.Rd':
  \usage lines wider than 90 characters:
     fast.flexsim(scale = 2, island,dispersalscale = 51, allee = 1, T = 1000, initp,parcombination, spnum = 2, sourcetype = "constant", type ... [TRUNCATED]

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

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

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

These lines will be truncated in the PDF manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/coffee.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’
Packages required but not available: 'graph', 'Rgraphviz'

Package suggested but not available for checking: ‘car’

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

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

Package suggested but not available for checking: ‘mstate’

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CoImp.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: ‘coin’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cointmonitoR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cold.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/colf.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CollapseLevels.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'plm', 'vars'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘furrr’
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘collectArgs_and_iterateWithArgs.Rmd’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘fda’

Package suggested but not available for checking: ‘maxLik’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/collUtils.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: 'viridis', 'susieR'

Package suggested but not available for checking: ‘snpStats’

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

Package suggested but not available for checking: ‘devtools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/coloredICA.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.
Malformed Title field: should not end in a period.
Package in Depends field not imported from: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plotVenn2d : twoWayOverlap: no visible global function definition for
  ‘grid.polygon’
plotVenn2d : twoWayOverlap: no visible global function definition for
  ‘gpar’
plotVenn2d: no visible global function definition for ‘grid.text’
plotVenn2d: no visible global function definition for ‘gpar’
plotVenn2d: no visible global function definition for ‘grid.polygon’
plotVenn3d : twoWayOverlap: no visible global function definition for
  ‘grid.polygon’
plotVenn3d : twoWayOverlap: no visible global function definition for
  ‘gpar’
plotVenn3d: no visible global function definition for ‘grid.text’
plotVenn3d: no visible global function definition for ‘gpar’
plotVenn3d: no visible global function definition for ‘grid.polygon’
plotVenn4d : getCommonEllipse: no visible global function definition
  for ‘aggregate’
plotVenn4d : region.polygon: no visible global function definition for
  ‘head’
plotVenn4d : region.polygon: no visible global function definition for
  ‘grid.polygon’
plotVenn4d : region.polygon: no visible global function definition for
  ‘gpar’
plotVenn4d: no visible global function definition for ‘grid.text’
plotVenn4d: no visible global function definition for ‘gpar’
plotVenn4d: no visible global function definition for ‘pushViewport’
plotVenn4d: no visible global function definition for ‘viewport’
plotVenn4d: no visible global function definition for ‘grid.polygon’
plotVenn4d: no visible global function definition for ‘upViewport’
resizeCircles: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  aggregate gpar grid.polygon grid.text head pushViewport uniroot
  upViewport viewport
Consider adding
  importFrom("stats", "aggregate", "uniroot")
  importFrom("utils", "head")
to your NAMESPACE file.
Package required but not available: ‘raster’

Package suggested but not available for checking: ‘tigris’

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
generateMonochromaticColors: no visible global function definition for
  ‘col2rgb’
generateMonochromaticColors: no visible global function definition for
  ‘rgb’
generateMonochromaticColors: no visible global function definition for
  ‘tail’
hsv2rgb: no visible global function definition for ‘rgb’
rotational_dispersion: no visible global function definition for
  ‘col2rgb’
rotational_dispersion: no visible global function definition for
  ‘rgb2hsv’
tetradicColors: no visible global function definition for ‘head’
triadicColors: no visible global function definition for ‘head’
Undefined global functions or variables:
  col2rgb head rgb rgb2hsv tail
Consider adding
  importFrom("grDevices", "col2rgb", "rgb", "rgb2hsv")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘plotly’
Malformed Description field: should contain one or more complete sentences.
primary.colors: no visible global function definition for ‘rgb’
rgb.tables: no visible global function definition for ‘rgb’
ygobb: no visible global function definition for ‘approx’
ygobb: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  approx rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "approx")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'vcd', 'viridis'
Errors in running code in vignettes:
when running code in ‘hcl-colors.Rnw’
  ...

> options(prompt = "R> ", continue = "+  ")

> library("colorspace")

> library("vcd")

  When sourcing ‘hcl-colors.R’:
Error: there is no package called ‘vcd’
Execution halted

  ‘hcl-colors.Rnw’... failed
Error(s) in re-building vignettes:
  ...
--- re-building ‘colorspace.Rmd’ using rmarkdown
--- finished re-building ‘colorspace.Rmd’

--- re-building ‘hcl-colors.Rnw’ using Sweave

Error: processing vignette ‘hcl-colors.Rnw’ failed with diagnostics:
 chunk 1 (label = preliminaries) 
Error in library("vcd") : there is no package called ‘vcd’

--- failed re-building ‘hcl-colors.Rnw’

SUMMARY: processing the following file failed:
  ‘hcl-colors.Rnw’

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘httptest’
Running ‘test-all.R’ [1s/2s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > test_check("colourlovers")
  Loading required package: colourlovers
  Error in library(httptest) : there is no package called 'httptest'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘clusterSim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/COMBAT.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
competitive.test: no visible global function definition for ‘runif’
selfcontained.test : fun2: no visible global function definition for
  ‘qchisq’
selfcontained.test: no visible global function definition for ‘cov’
selfcontained.test: no visible global function definition for ‘qchisq’
selfcontained.test: no visible global function definition for ‘cor’
selfcontained.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cor cov pchisq qchisq runif
Consider adding
  importFrom("stats", "cor", "cov", "pchisq", "qchisq", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘devtools’

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.
Found the following files/directories:
  ‘cometExactTest_plot.pdf’
Package required but not available: ‘R.utils’

Package suggested but not available for checking: ‘httptest’

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: ‘glmnet’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'diagram', 'GGally', 'useful', 'wrassp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Comp2ROC.Rcheck/00install.out’ for details.
Package required but not available: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
addxaxis: no visible global function definition for ‘par’
addxaxis: no visible global function definition for ‘axis’
addxaxis: no visible global function definition for ‘mtext’
eplot: no visible global function definition for ‘par’
eplot: no visible global function definition for ‘axis’
eplot: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  axis mtext par
Consider adding
  importFrom("graphics", "axis", "mtext", "par")
to your NAMESPACE file.
Package required but not available: ‘expm’

Packages suggested but not available for checking:
  'pcalg', 'InvariantCausalPrediction', 'glmnet', 'CAM', 'mboost',
  'flare'

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

Package suggested but not available for checking: ‘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/compareODM.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'GGally', 'DiceOptim'
Running examples in ‘comparer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hype
> ### Title: Hyperparameter optimization
> ### Aliases: hype
> 
> ### ** Examples
> 
> 
> # Have df output, but only use one value from it
> h1 <- hype$new(
+   eval_func = function(a, b) {data.frame(c=a^2+b^2, d=1:2)},
+   extract_output_func = function(odf) {odf$c[1]},
+   a = par_unif$new('a', -1, 2),
+   b = par_unif$new('b', -10, 10),
+   n_lhs = 10
+ )
> h1$run_all()
Running 1, completed 0/10 Sat Apr 30 14:00:15 2022
$a
[1] -0.5073135

$b
[1] 6.54052

Running 2, completed 1/10 Sat Apr 30 14:00:15 2022
$a
[1] 1.362881

$b
[1] 3.985368

Running 3, completed 2/10 Sat Apr 30 14:00:15 2022
$a
[1] -0.7663256

$b
[1] -0.7330135

Running 4, completed 3/10 Sat Apr 30 14:00:15 2022
$a
[1] 1.039193

$b
[1] 0.4264163

Running 5, completed 4/10 Sat Apr 30 14:00:15 2022
$a
[1] 0.6365823

$b
[1] -5.741255

Running 6, completed 5/10 Sat Apr 30 14:00:15 2022
$a
[1] 0.02302522

$b
[1] -9.043764

Running 7, completed 6/10 Sat Apr 30 14:00:15 2022
$a
[1] 1.643261

$b
[1] -6.151851

Running 8, completed 7/10 Sat Apr 30 14:00:15 2022
$a
[1] 0.38148

$b
[1] 9.197522

Running 9, completed 8/10 Sat Apr 30 14:00:15 2022
$a
[1] 1.896417

$b
[1] 5.952341

Running 10, completed 9/10 Sat Apr 30 14:00:15 2022
$a
[1] -0.2940408

$b
[1] -2.536415

> h1$add_EI(n = 1)
Error in loadNamespace(x) : there is no package called ‘DiceOptim’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: ‘cmprsk’

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.
Package required but not available: ‘fExtremes’

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

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

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

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/complexity.Rcheck/00install.out’ for details.
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/CompLognormal.Rcheck/00install.out’ for details.
Skipping vignette re-building
Packages suggested but not available for checking: 'R.rsp', 'laGP'

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/COMPoissonReg.Rcheck/00install.out’ for details.
Packages required but not available:
  'codalm', 'Directional', 'doParallel', 'emplik', 'glmnet', 'mda',
  'mixture', 'NlcOptim', 'pchc', 'Rfast', 'Rfast2', 'sn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'otsad', 'tsoutliers', 'forecast', 'anomalize', 'ICS'

Package suggested but not available for checking: ‘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/compound.Cox.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/Compounding.Rcheck/00install.out’ for details.
Packages required but not available: 'RandomFields', 'fields', 'mapproj'

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/CompR.Rcheck/00install.out’ for details.
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
kef: no visible global function definition for ‘dgamma’
kef: no visible global function definition for ‘dlnorm’
simp_int: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dgamma dlnorm
Consider adding
  importFrom("stats", "approx", "dgamma", "dlnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘qualV’

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/ConConPiWiFun.Rcheck/00install.out’ for details.
Package required but not available: ‘Rglpk’

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CONCUR.Rcheck/00install.out’ for details.
Packages required but not available: 'metafor', 'survminer'

Packages suggested but not available for checking:
  'lme4', 'rms', 'brms', 'rstan', 'rstanarm', 'daewr'

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
K1.norm: no visible global function definition for ‘dnorm’
K1.norm: no visible global function definition for ‘pnorm’
K1.t3: no visible global function definition for ‘pt’
K2.norm: no visible global function definition for ‘dnorm’
K2.norm: no visible global function definition for ‘pnorm’
K2.t3: no visible global function definition for ‘pt’
Undefined global functions or variables:
  dnorm pnorm pt
Consider adding
  importFrom("stats", "dnorm", "pnorm", "pt")
to your NAMESPACE file.
Packages required but not available: 'quantregForest', 'RPtests'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/condmixt.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/condMVNorm.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'csampling', 'marg', 'nlreg'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cond.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
ml_solver: no visible global function definition for ‘approx’
select_kmax: no visible global function definition for ‘median’
Undefined global functions or variables:
  approx median
Consider adding
  importFrom("stats", "approx", "median")
to your NAMESPACE file.
Packages required but not available: 'np', 'doParallel', 'doRNG'

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

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

Package suggested but not available for checking: ‘RSQLite’

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

Packages suggested but not available for checking:
  'hdrcde', 'scagnostics', 'ks', 'mlr', 'C50', 'bartMachine', 'caret',
  'glmnet', 'glmnetUtils', 'mlr3'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'scagnostics', 'hdrcde', 'DendSer'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ConfigParser.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 suggested but not available for checking: 'rstanarm', 'brms'
Error(s) in re-building vignettes:
  ...
--- re-building ‘conformalbayes.Rmd’ using rmarkdown
Quitting from lines 27-42 (conformalbayes.Rmd) 
Error: processing vignette ‘conformalbayes.Rmd’ failed with diagnostics:
there is no package called 'rstanarm'
--- failed re-building ‘conformalbayes.Rmd’

SUMMARY: processing the following file failed:
  ‘conformalbayes.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: 'fda', 'future.apply', 'ggpubr'

Package suggested but not available for checking: ‘roahd’

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

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

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.
Packages required but not available: 'STAR', 'fitdistrplus'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘penalized’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘confSAM.Rmd’ using rmarkdown
Quitting from lines 77-79 (confSAM.Rmd) 
Error: processing vignette ‘confSAM.Rmd’ failed with diagnostics:
there is no package called 'penalized'
--- failed re-building ‘confSAM.Rmd’

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

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

Package suggested but not available for checking: ‘FeatureTerminatoR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'phangorn', 'Quartet', 'TreeSearch'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/conicfit.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
conicPlot: no visible global function definition for ‘palette’
conicPlotAsymptotes: no visible global function definition for
  ‘palette’
conicPlotAsymptotes: no visible global function definition for ‘abline’
conicPlotAxes: no visible global function definition for ‘palette’
conicPlotAxes: no visible global function definition for ‘abline’
plotDegenerateConic: no visible global function definition for ‘points’
plotDegenerateConic: no visible global function definition for ‘abline’
plotEllipsis: no visible global function definition for ‘lines’
plotEllipsis: no visible global function definition for ‘points’
plotHyperbola: no visible global function definition for ‘lines’
plotHyperbola: no visible global function definition for ‘points’
plotParabola: no visible global function definition for ‘lines’
Undefined global functions or variables:
  abline lines palette points
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "lines", "points")
to your NAMESPACE file.
Packages required but not available: 'ppcor', 'miceadds'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
‘library’ or ‘require’ call to ‘parallel’ which was already attached by Depends.
  Please remove these calls from your code.
‘library’ or ‘require’ calls in package code:
  ‘Rmpi’ ‘snow’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ConjointChecks: no visible global function definition for ‘makeCluster’
ConjointChecks: no visible global function definition for
  ‘clusterSetRNGStream’
ConjointChecks: no visible global function definition for
  ‘clusterApply’
ConjointChecks: no visible global function definition for ‘stopCluster’
omni.check: no visible global function definition for ‘runif’
omni.check: no visible global function definition for ‘quantile’
plot.checks: no visible global function definition for ‘mtext’
plot.checks: no visible global function definition for ‘text’
Undefined global functions or variables:
  clusterApply clusterSetRNGStream makeCluster mtext quantile runif
  stopCluster text
Consider adding
  importFrom("graphics", "mtext", "text")
  importFrom("stats", "quantile", "runif")
to your NAMESPACE file.
Packages required but not available: 'fpc', 'ggfortify'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rmgarch', 'frequencyConnectedness', 'quantreg', 'glmnet', 'xts',
  'rugarch'

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.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ComplexHeatmap', 'dendextend', 'ggrepel', 'irlba', 'leidenAlg',
  'Matrix.utils', 'N2R', 'sccore'

Packages suggested but not available for checking:
  'AnnotationDbi', 'conosPanel', 'DESeq2', 'ggrastr', 'GO.db',
  'org.Hs.eg.db', 'org.Mm.eg.db', 'p2data', 'pagoda2', 'Seurat',
  'SummarizedExperiment', 'uwot'

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.
Packages required but not available:
  'raster', 'fields', 'rgdal', 'rgeos', 'doSNOW'

Package suggested but not available for checking: ‘alphahull’

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

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ConSpline.Rcheck/00install.out’ for details.
Package required but not available: ‘ConsRank’

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

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

Package suggested but not available for checking: ‘spdep’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘vroom’
Package required but not available: ‘text2vec’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rmpfr', 'go2bigq'

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cf
> ### Title: Make contour plot from data or function
> ### Aliases: cf
> 
> ### ** Examples
> 
> cf(function(x){x[1]^2 - x[2]})
> x <- runif(20)
> y <- runif(20)
> z <- exp(-(x-.5)^2-5*(y-.5)^2)# + rnorm(20,0,.05)
> cf(x,y,z)
Error in loadNamespace(x) : there is no package called ‘laGP’
Calls: cf ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [47s/73s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ContourFunctions)
  > 
  > test_check("ContourFunctions")
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 51 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-gcf_grid.R:51:3): gcf_data ──────────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'laGP'
  Backtrace:
      ▆
   1. ├─ContourFunctions::gcf_data(x, y, z) at test-gcf_grid.R:51:2
   2. │ └─ContourFunctions::cf_data(...)
   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-gcf_grid.R:68:3): gcf ───────────────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'laGP'
  Backtrace:
      ▆
   1. ├─ContourFunctions::gcf_data(x, y, z) at test-gcf_grid.R:68:2
   2. │ └─ContourFunctions::cf_data(...)
   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-nongg.R:33:3): cf_data ──────────────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'laGP'
  Backtrace:
      ▆
   1. ├─ContourFunctions::cf_data(x, y, z) at test-nongg.R:33:2
   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 3 | WARN 0 | SKIP 0 | PASS 51 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_the_cf_R_package.Rmd’ using rmarkdown
Quitting from lines 75-81 (Introduction_to_the_cf_R_package.Rmd) 
Error: processing vignette ‘Introduction_to_the_cf_R_package.Rmd’ failed with diagnostics:
there is no package called 'laGP'
--- failed re-building ‘Introduction_to_the_cf_R_package.Rmd’

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

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

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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/contTimeCausal.Rcheck/00install.out’ for details.
Package required but not available: ‘SHELF’

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ConvergenceConcepts.Rcheck/00install.out’ for details.
Packages required but not available: 'eurostat', 'ggpubr'

Packages suggested but not available for checking:
  'devtools', 'readr', 'tidyverse'

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

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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'phytools', 'geiger'

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

Package suggested but not available for checking: ‘RSQLite’

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

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

Package suggested but not available for checking: ‘imager’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'magicaxis', 'celestial', 'raster', 'bit64'

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: 'GameTheory', 'kappalab'

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

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

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

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/copCAR.Rcheck/00install.out’ for details.
Packages required but not available: 'msm', 'copBasic'

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’

Packages suggested but not available for checking:
  'fitbitViz', 'tmap', 'leaflet', 'leafgl'

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

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:
  'caret', 'flexsurv', 'icenReg', 'plotly'

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

Package suggested but not available for checking: ‘Rmisc’

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

Package suggested but not available for checking: ‘cec2005benchmark’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Copula.Markov.survival.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'Rmpfr', 'lcopula', 'mev', 'qrng', 'randtoolbox', 'rugarch',
  'tseries'
Package required but not available: ‘rvinecopulib’

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
Packages suggested but not available for checking: 'mpmi', 'fitdistrplus'
checkRd: (7) p_combine.Rd:20: \item in \value must have non-empty label
checkRd: (7) p_combine.Rd:23: \item in \value must have non-empty label
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/corclass.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: ‘StatMatch’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/corehunter.Rcheck/00install.out’ for details.
Package required but not available: ‘rpart.plot’

Package suggested but not available for checking: ‘ExplainPrediction’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
advanceRNG: no visible global function definition for ‘runif’
randomEventMoves: no visible global function definition for ‘runif’
randomRescaledEventMoves: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: ‘car’
Running examples in ‘coreSim-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: b_sim
> ### Title: Simulate coefficients from a GLM by making draws from the
> ###   multivariate normal distribution
> ### Aliases: b_sim
> 
> ### ** Examples
> 
> library(car)
Error in library(car) : there is no package called ‘car’
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(coreSim)
  > library(car)
  Error in library(car) : there is no package called 'car'
  Execution halted
Malformed Description field: should contain one or more complete sentences.
coreTDT_geneset: no visible global function definition for
  ‘write.table’
pvalue_calculator: no visible global function definition for ‘dbinom’
Undefined global functions or variables:
  dbinom write.table
Consider adding
  importFrom("stats", "dbinom")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Packages required but not available:
  'expm', 'phangorn', 'viridis', 'Rmpfr', '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/corkscrew.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rdisop’

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

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: 'SpatialTools', 'vcd'

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

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

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

Packages suggested but not available for checking: 'plotly', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘tm’
Packages required but not available: 'wordcloud', 'RNewsflow'

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

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

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: ‘ProData’
Package suggested but not available for checking: ‘xcms’
Package required but not available: ‘diagram’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'BayesFactor', 'ggcorrplot', 'ggraph', 'Hmisc', 'lme4', 'ppcor',
  'rstanarm', 'WRS2'
Package required but not available: ‘Rmpfr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘seriation’
Running ‘testthat.R’ [21s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(corrgram)
  > 
  > test_check("corrgram")
  [ FAIL 1 | WARN 880 | SKIP 0 | PASS 19 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_misc.R:53:3): order argument ────────────────────────────────────
  Error in `corrgram(mtcars, order = "GW")`: Please use install.packages('seriation') for this 'order' option.
  Backtrace:
      ▆
   1. └─corrgram::corrgram(mtcars, order = "GW") at test_misc.R:53:2
  
  [ FAIL 1 | WARN 880 | SKIP 0 | PASS 19 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CorrMixed.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘seriation’
Error(s) in re-building vignettes:
  ...
--- re-building ‘corrplot-intro.Rmd’ using rmarkdown
Quitting from lines 167-180 (corrplot-intro.Rmd) 
Error: processing vignette ‘corrplot-intro.Rmd’ failed with diagnostics:
there is no package called 'seriation'
--- failed re-building ‘corrplot-intro.Rmd’

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

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

Package suggested but not available for checking: ‘RSQLite’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
corr.Qmatrix: no visible global function definition for ‘cor’
corr.Qmatrix: no visible global function definition for ‘cor.test’
summarise.Fst: no visible global function definition for ‘cor’
summarise.Fst: no visible global function definition for ‘sd’
summarise.lnPD: no visible global function definition for ‘sd’
Undefined global functions or variables:
  cor cor.test sd
Consider adding
  importFrom("stats", "cor", "cor.test", "sd")
to your NAMESPACE file.
Rd file 'corr.Qmatrix.Rd':
  \usage lines wider than 90 characters:
     corr.Qmatrix(filepath = "./", instruct = FALSE, rowncol = TRUE, avmax = TRUE, pvalue = FALSE, raw = TRUE, r = 0.99, p = 0.05)

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

These lines will be truncated in the PDF manual.
Packages required but not available: 'BinNonNor', 'BinOrdNonNor', 'GenOrd'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'forecast', 'hts'
Packages required but not available: 'clusterGeneration', 'Biobase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
dist: no visible global function definition for ‘quantile’
edgecount: no visible global function definition for ‘reshape’
edgecutoff: no visible global function definition for ‘boxplot’
edgecutoff: no visible global function definition for ‘sd’
edgecutoff: no visible global function definition for ‘median’
edgecutoff: no visible global function definition for ‘IQR’
Undefined global functions or variables:
  IQR boxplot median quantile reshape sd
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "IQR", "median", "quantile", "reshape", "sd")
to your NAMESPACE file.
Package required but not available: ‘furrr’

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

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/COSINE.Rcheck/00install.out’ for details.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
cosinor.lm: no visible binding for global variable ‘na.omit’
cosinor.lm: no visible global function definition for ‘terms’
cosinor.lm: no visible global function definition for ‘as.formula’
cosinor.lm: no visible global function definition for ‘lm’
cosinor_analyzer: no visible binding for global variable ‘vitamind’
cosinor_analyzer : <anonymous>: no visible global function definition
  for ‘as.formula’
ggplot.cosinor.lm: no visible global function definition for ‘predict’
predict.cosinor.lm: no visible global function definition for ‘fitted’
predict.cosinor.lm: no visible global function definition for ‘predict’
simulate_cosinor: no visible global function definition for ‘runif’
simulate_cosinor: no visible global function definition for ‘rbinom’
simulate_cosinor: no visible global function definition for ‘rnorm’
summary.cosinor.lm: no visible global function definition for ‘vcov’
summary.cosinor.lm: no visible global function definition for ‘qnorm’
summary.cosinor.lm: no visible global function definition for ‘pnorm’
test_cosinor: no visible global function definition for ‘pchisq’
test_cosinor: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula fitted lm na.omit pchisq pnorm predict qnorm rbinom rnorm
  runif terms vcov vitamind
Consider adding
  importFrom("stats", "as.formula", "fitted", "lm", "na.omit", "pchisq",
             "pnorm", "predict", "qnorm", "rbinom", "rnorm", "runif",
             "terms", "vcov")
to your NAMESPACE file.
Package suggested but not available for checking: ‘ICAMS’
Malformed Title field: should not end in a period.
D.M: no visible global function definition for ‘integrate’
lookbackTime: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
Rd file 'mass.CO.Rd':
  \usage lines wider than 90 characters:
     mass.CO(intInt, z, alpha = 0.8, f.rest = 115.27, omega.m = 0.27, omega.lambda = 0.73, H.0 = 71)

These lines will be truncated in the PDF manual.
Package required but not available: ‘mAr’

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

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/COST.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'ctsem', 'MBESS', 'doParallel', 'zcurve', 'scholar'

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: 'tram', 'mlt', 'basefun', 'alabama'

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

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/couchDB.Rcheck/00install.out’ for details.
Package required but not available: ‘colordistance’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'quantreg', 'Hmisc', '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/countgmifs.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘msme’

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

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

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 required but not available: 'dataRetrieval', 'R.utils'

Package suggested but not available for checking: ‘hurricaneexposure’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/covBM.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘qgraph’
Error(s) in re-building vignettes:
  ...
--- re-building ‘CovCombR.rmd’ using rmarkdown
Quitting from lines 66-68 (CovCombR.rmd) 
Error: processing vignette ‘CovCombR.rmd’ failed with diagnostics:
there is no package called 'qgraph'
--- failed re-building ‘CovCombR.rmd’

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

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

Packages suggested but not available for checking:
  'ggrepel', 'plotly', 'gamlss.dist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘covfefe_inauguration.txt’
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.
Packages suggested but not available for checking:
  'ggrepel', 'leaflet', 'plotly', 'tidyverse'
Error(s) in re-building vignettes:
  ...
--- re-building ‘covid19br.Rmd’ using rmarkdown
Quitting from lines 36-50 (covid19br.Rmd) 
Error: processing vignette ‘covid19br.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘covid19br.Rmd’

--- re-building ‘election2018.Rmd’ using rmarkdown
Quitting from lines 21-42 (election2018.Rmd) 
Error: processing vignette ‘election2018.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘election2018.Rmd’

--- re-building ‘maps.Rmd’ using rmarkdown
Quitting from lines 23-38 (maps.Rmd) 
Error: processing vignette ‘maps.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘maps.Rmd’

SUMMARY: processing the following files failed:
  ‘covid19br.Rmd’ ‘election2018.Rmd’ ‘maps.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: ‘EpiEstim’

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

Package suggested but not available for checking: ‘readr’

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: 'RSQLite', 'wbstats'

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

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 required but not available: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘httptest’
Running ‘testthat.R’ [14s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(covidcast)
  We encourage COVIDcast API users to register on our mailing list:
  https://lists.andrew.cmu.edu/mailman/listinfo/delphi-covidcast-api
  We'll send announcements about new data sources, package updates,
  server maintenance, and new features.
  > 
  > test_check("covidcast")
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  [ FAIL 1 | WARN 1 | SKIP 7 | PASS 38 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • (R.Version()$major != "4") | (R.Version()$minor != "0.3") is TRUE (1)
  • On CRAN (6)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-covidcast.R:1:1): (code run outside of `test_that()`) ───────────
  <packageNotFoundError/error/condition>
  Error in `library(httptest)`: there is no package called 'httptest'
  Backtrace:
      ▆
   1. └─base::library(httptest) at test-covidcast.R:1:0
  
  [ FAIL 1 | WARN 1 | SKIP 7 | PASS 38 ]
  Error: Test failures
  Execution halted
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.
Packages required but not available: 'seqinr', 'ggpubr', 'VennDiagram'

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

Packages suggested but not available for checking: 'ggspatial', 'rworldmap'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
covreg.mcmc: no visible global function definition for ‘model.frame’
covreg.mcmc: no visible global function definition for ‘model.matrix’
covreg.mcmc: no visible global function definition for ‘model.response’
covreg.mcmc: no visible global function definition for ‘lm’
covreg.mcmc: no visible global function definition for ‘rnorm’
covreg.mcmc: no visible global function definition for ‘cov’
rmn: no visible global function definition for ‘rnorm’
rwish: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  cov lm model.frame model.matrix model.response rnorm
Consider adding
  importFrom("stats", "cov", "lm", "model.frame", "model.matrix",
             "model.response", "rnorm")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'dr', 'np'

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'PASWR', 'VennDiagram'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rms', 'mediation'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘kinship2’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/coxme.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CoxPhLb.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/coxphSGD.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/coxphw.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CoxPlus.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CoxR2.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'MESS', 'multtest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages suggested but not available for checking: 'doRNG', 'doParallel'
Package required but not available: ‘forestplot’

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 required but not available: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'multiway', '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/CpGassoc.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘glmnet’
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(CPGLIB)
  > 
  > test_check("CPGLIB")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_cv_function.R:8:1): (code run outside of `test_that()`) ─────────
  <packageNotFoundError/error/condition>
  Error in `library(glmnet)`: there is no package called 'glmnet'
  Backtrace:
      ▆
   1. └─base::library(glmnet) at test_cv_function.R:8:0
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'mlr3', 'knockoff'

Packages suggested but not available for checking:
  'BEST', 'mlr3learners', 'glmnet', 'doParallel'

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

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

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

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: 'prodlim', 'tpr'

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: ‘Rfast’

Package suggested but not available for checking: ‘L1pack’

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: ‘readr’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (7) capitais.Rd:29: invalid email address: <rpradosiqueira@gmail.com>
checkRd: (7) condicoes_tempo.Rd:23: invalid email address: <rpradosiqueira@gmail.com>
checkRd: (7) estacoes_metar.Rd:25: invalid email address: <rpradosiqueira@gmail.com>
checkRd: (7) estendidaLatLon.Rd:35: invalid email address: <rpradosiqueira@gmail.com>
checkRd: (7) iuv.Rd:30: invalid email address: <rpradosiqueira@gmail.com>
checkRd: (7) listaCidades.Rd:28: invalid email address: <rpradosiqueira@gmail.com>
checkRd: (7) metar.Rd:32: invalid email address: <rpradosiqueira@gmail.com>
checkRd: (7) ondas.Rd:44: invalid email address: <rpradosiqueira@gmail.com>
checkRd: (7) prev4dias.Rd:33: invalid email address: <rpradosiqueira@gmail.com>
checkRd: (7) prev7dias.Rd:30: invalid email address: <rpradosiqueira@gmail.com>
checkRd: (7) prevEstendida.Rd:32: invalid email address: <rpradosiqueira@gmail.com>
checkRd: (7) prevLatLon.Rd:35: invalid email address: <rpradosiqueira@gmail.com>
'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 suggested but not available for checking: ‘leaflet’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 399-421 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
there is no package called 'leaflet'
--- 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: ‘quantreg’

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.
distance.comoving: no visible global function definition for
  ‘integrate’
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
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/cramer.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: 'wordcloud', 'tm'

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

Packages suggested but not available for checking:
  'rgdal', 'argosfilter', 'xts', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'glmx', 'lmtest', 'memisc'
Error(s) in re-building vignettes:
  ...
--- re-building ‘crch.Rnw’ using Sweave

Error: processing vignette ‘crch.Rnw’ failed with diagnostics:
 chunk 11 
Error in library("glmx") : there is no package called ‘glmx’

--- failed re-building ‘crch.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'fastglm', 'ggpubr', 'lme4'

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

Packages suggested but not available for checking: 'pdp', 'pmml'

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

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

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

Packages suggested but not available for checking:
  'AnnotationDbi', 'org.Hs.eg.db', 'clusterProfiler'

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

Package suggested but not available for checking: ‘pals’

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

Packages suggested but not available for checking:
  'gghighlight', 'showtext', 'tidyverse'

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 required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fields’
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
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:
  'Biostrings', 'GenomicRanges', 'IRanges', 'GenomeInfoDb',
  'S4Vectors', 'rtracklayer', 'vtreat'

Package suggested but not available for checking: ‘BSgenome.Scerevisiae.UCSC.sacCer2’

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

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

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

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

Package suggested but not available for checking: ‘ggmcmc’

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/crn.Rcheck/00install.out’ for details.
'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.
Package required but not available: ‘imager’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cumulative
> ### Title: Sum of a weather variable between between two dates
> ### Aliases: cumulative
> 
> ### ** Examples
> 
> ## Selected calculations
> library(tidyverse)
Error in library(tidyverse) : there is no package called ‘tidyverse’
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(purrr)
  > library(testthat)
  
  Attaching package: 'testthat'
  
  The following object is masked from 'package:purrr':
  
      is_null
  
  > library(tidyverse)
  Error in library(tidyverse) : there is no package called 'tidyverse'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘crop-grow-days.Rmd’ using rmarkdown
Quitting from lines 34-37 (./../man/fragments/intro.Rmd) 
Quitting from lines 11-17 (./../man/fragments/intro.Rmd) 
Error: processing vignette ‘crop-grow-days.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘crop-grow-days.Rmd’

--- re-building ‘getting-weather-data.Rmd’ using rmarkdown
Quitting from lines 34-37 (./../man/fragments/intro.Rmd) 
Quitting from lines 11-17 (./../man/fragments/intro.Rmd) 
Error: processing vignette ‘getting-weather-data.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘getting-weather-data.Rmd’

SUMMARY: processing the following files failed:
  ‘crop-grow-days.Rmd’ ‘getting-weather-data.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘crop.eps’ ‘crop.pdf’ ‘crop.png’ ‘crop.ps’
Package required but not available: ‘raster’

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.
Packages required but not available: 'raster', '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/crossdes.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘furrr’
Running examples in ‘crossmap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: future_map_vec
> ### Title: Parallelized mapping functions that automatically determine type
> ### Aliases: future_map_vec future_map2_vec future_pmap_vec future_imap_vec
> ###   future_xmap_vec
> 
> ### ** Examples
> 
> fruits   <- c("apple", "banana", "carrot", "durian", "eggplant")
> desserts <- c("bread", "cake", "cupcake", "streudel", "muffin")
> x        <- sample(5)
> y        <- sample(5)
> z        <- sample(5)
> names(z) <- fruits
> 
> future_map_vec(x, ~ . ^ 2)
Error in `require_package()`:
! `future_map_vec()` requires the 'furrr' package.
• Try `install.packages("furrr")`
Backtrace:
    ▆
 1. └─crossmap::future_map_vec(x, ~.^2)
 2.   └─crossmap:::require_furrr()
 3.     └─crossmap:::require_package("furrr", fn = fn)
 4.       └─rlang::abort(...)
Execution halted
Running ‘testthat.R’ [8s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(crossmap)
  > 
  > test_check("crossmap")
  [ FAIL 1 | WARN 0 | SKIP 20 | PASS 189 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • furrr cannot be loaded (20)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-errors.R:25:3): message for no plan ─────────────────────────────
  Error in `require_package("furrr", fn = fn)`: `eval_bare()` requires the 'furrr' package.
  • Try `install.packages("furrr")`
  Backtrace:
      ▆
   1. ├─testthat::expect_message(require_furrr(), "not set up to run background processes") at test-errors.R:25:2
   2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)
   3. │   ├─testthat .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─crossmap:::require_furrr()
   7.   └─crossmap:::require_package("furrr", fn = fn)
   8.     └─rlang::abort(...)
  
  [ FAIL 1 | WARN 0 | SKIP 20 | PASS 189 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘nbpMatching’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
BootC : BSs: no visible global function definition for ‘lm’
BootC : BSs: no visible global function definition for ‘vcov’
BootC: no visible global function definition for ‘boot’
BootC: no visible global function definition for ‘boot.ci’
DeltaC: no visible global function definition for ‘lm’
DeltaC: no visible global function definition for ‘vcov’
FiellerC: no visible global function definition for ‘lm’
FiellerC: no visible global function definition for ‘vcov’
nonLinearC: no visible global function definition for ‘nls’
Undefined global functions or variables:
  boot boot.ci lm nls vcov
Consider adding
  importFrom("stats", "lm", "nls", "vcov")
to your NAMESPACE file.
Package required but not available: ‘Rmpfr’

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

Package suggested but not available for checking: ‘Biobase’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'sda', 'care', 'binda'
Package suggested but not available for checking: ‘openVA’
Error(s) in re-building vignettes:
  ...
--- re-building ‘using-crossva-and-openva.Rmd’ using rmarkdown
Quitting from lines 14-17 (using-crossva-and-openva.Rmd) 
Error: processing vignette ‘using-crossva-and-openva.Rmd’ failed with diagnostics:
there is no package called 'openVA'
--- failed re-building ‘using-crossva-and-openva.Rmd’

SUMMARY: processing the following file failed:
  ‘using-crossva-and-openva.Rmd’

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

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

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

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

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/crrSC.Rcheck/00install.out’ for details.
Package required but not available: ‘cmprsk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/crso.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: 'np', 'quantreg'

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

Packages suggested but not available for checking:
  'mapboxapi', 'tigris', 'tidycensus'

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

Package suggested but not available for checking: ‘adabag’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CRTgeeDR.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'crunchy', 'devtools', 'haven', 'httptest', 'styler'
Running ‘spelling.R’ [0s/1s]
  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
Package suggested but not available for checking: ‘httptest’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/crunchy.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: 'mapdata', 'marmap', 'swfscDAS'

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

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

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

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: ‘flux’

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

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

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

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.
Package required but not available: ‘exactci’

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

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

Package suggested but not available for checking: ‘plotly’

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 required but not available: ‘Biostrings’

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

Package suggested but not available for checking: ‘viridis’

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

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

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

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'multiApply', 's2dv', 'ClimProjDiags'

Package suggested but not available for checking: ‘CSTools’

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

Package suggested but not available for checking: ‘tmap’

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

Package suggested but not available for checking: ‘ggraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
pielou: 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: ‘sna’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cstab.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
cstar: no visible global function definition for ‘vcov’
cstar : utility: no visible global function definition for ‘dt’
cstar : maximand: no visible global function definition for ‘integrate’
cstar: no visible global function definition for ‘uniroot’
cstari : utility: no visible global function definition for ‘dt’
cstari : maximand: no visible global function definition for
  ‘integrate’
cstari: no visible global function definition for ‘uniroot’
cstarme : utility: no visible global function definition for ‘density’
cstarme : maximand: no visible global function definition for
  ‘integrate’
cstarme : maximand: no visible global function definition for ‘sd’
cstarme: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  density dt integrate sd uniroot vcov
Consider adding
  importFrom("stats", "density", "dt", "integrate", "sd", "uniroot",
             "vcov")
to your NAMESPACE file.
Package required but not available: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'qmap', 'easyVerification', 's2dverification', 's2dv', 'multiApply',
  'ClimProjDiags', 'verification'

Package suggested but not available for checking: ‘startR’

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 required but not available:
  'doParallel', 'relaxo', 'caret', 'glmnet', 'HDCI'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘bit64’
'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: ‘vcd’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘mirt’

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

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

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', 'fda', 'gdistance'

Packages suggested but not available for checking: 'dismo', 'crawl'

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

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

Packages suggested but not available for checking: 'bit64', 'move'

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

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

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

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

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

Packages suggested but not available for checking: 'car', 'lmtest'

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

Packages suggested but not available for checking:
  'devtools', 'RSQLite', '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.
Package required but not available: ‘ctsem’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'rpart.plot', '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/CTTinShiny.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘Hello.csv’
Package required but not available: ‘ltm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Package required but not available: ‘styler’

Packages suggested but not available for checking:
  'rmapshaper', 'GGally', 'ggrepel', 'ggforce'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'seqinr', 'EMCluster'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cubfits.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘tidyrules’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Cubist.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CUB.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘glmnet’
Running examples in ‘cuda.ml-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cuda_ml_elastic_net
> ### Title: Train a linear model using elastic regression.
> ### Aliases: cuda_ml_elastic_net cuda_ml_elastic_net.default
> ###   cuda_ml_elastic_net.data.frame cuda_ml_elastic_net.matrix
> ###   cuda_ml_elastic_net.formula cuda_ml_elastic_net.recipe
> 
> ### ** Examples
> 
> 
> library(cuda.ml)
> 
> model <- cuda_ml_elastic_net(
+   formula = mpg ~ ., data = mtcars, alpha = 1e-3, l1_ratio = 0.6
+ )
> cuda_ml_predictions <- predict(model, mtcars)
> 
> # predictions will be comparable to those from a `glmnet` model with `lambda`
> # set to 1e-3 and `alpha` set to 0.6
> # (in `glmnet`, `lambda` is the weight of the penalty term, and `alpha` is
> #  the elastic mixing parameter between L1 and L2 penalties.
> 
> library(glmnet)
Error in library(glmnet) : there is no package called ‘glmnet’
Execution halted
Packages required but not available: 'xlsx', 'lmerTest', 'haven'

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/cumSeg.Rcheck/00install.out’ for details.
'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/curephEM.Rcheck/00install.out’ for details.
Packages required but not available: 'rstpm2', 'relsurv'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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: ‘ddalpha’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'feature', 'geometry', 'hdrcde', 'ks', 'ptinpoly'

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: ‘recipes’

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
Cut: no visible global function definition for ‘cor’
MissSimulation: no visible global function definition for ‘rbinom’
cutoff: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor rbinom
Consider adding
  importFrom("stats", "cor", "rbinom")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'doRNG', 'doParallel', 'pkgmaker'
Error(s) in re-building vignettes:
  ...
--- re-building ‘cutpointr.Rmd’ using rmarkdown
--- finished re-building ‘cutpointr.Rmd’

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

--- re-building ‘cutpointr_bootstrapping.Rmd’ using rmarkdown
Quitting from lines 182-202 (cutpointr_bootstrapping.Rmd) 
Error: processing vignette ‘cutpointr_bootstrapping.Rmd’ failed with diagnostics:
there is no package called 'doParallel'
--- failed re-building ‘cutpointr_bootstrapping.Rmd’

--- re-building ‘cutpointr_estimation.Rmd’ using rmarkdown
Assuming the positive class is yes
Assuming the positive class has higher x values
--- finished re-building ‘cutpointr_estimation.Rmd’

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
delta.glm: no visible global function definition for ‘glm’
delta.glm: no visible global function definition for ‘residuals’
delta.glm: no visible global function definition for ‘fitted’
delta.glm: no visible global function definition for ‘predict.glm’
two.stage.model.outputs: no visible global function definition for ‘sd’
Undefined global functions or variables:
  fitted glm predict.glm residuals sd
Consider adding
  importFrom("stats", "fitted", "glm", "predict.glm", "residuals", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: ‘lme4’
Error(s) in re-building vignettes:
  ...
--- re-building ‘FittingLogLinearModelsInCvam.Rnw’ using Sweave
--- finished re-building ‘FittingLogLinearModelsInCvam.Rnw’

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

Error: processing vignette ‘UnderstandingCoarsenedFactorsInCvam.Rnw’ failed with diagnostics:
 chunk 8 (label = "lme4") 
Error in library(lme4) : there is no package called ‘lme4’

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

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

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

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: ‘fGarch’

Package suggested but not available for checking: ‘PerformanceAnalytics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
calfun: no visible global function definition for ‘optim’
calfun: no visible global function definition for ‘cov’
calfun: no visible global function definition for ‘var’
Undefined global functions or variables:
  cov optim var
Consider adding
  importFrom("stats", "cov", "optim", "var")
to your NAMESPACE file.
Packages required but not available: 'origami', 'ggpubr'

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

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.
Package required but not available: ‘tableone’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages which this enhances but not available for checking:
  'gWidgets2', 'RGtk2'
Package suggested but not available for checking: ‘ggrepel’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CVEK.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ggbeeswarm’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘how_to_test_CVs.Rmd’ using rmarkdown
Quitting from lines 108-116 (how_to_test_CVs.Rmd) 
Error: processing vignette ‘how_to_test_CVs.Rmd’ failed with diagnostics:
there is no package called 'ggbeeswarm'
--- failed re-building ‘how_to_test_CVs.Rmd’

SUMMARY: processing the following file failed:
  ‘how_to_test_CVs.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/cvmdisc.Rcheck/00install.out’ for details.
Packages required but not available: 'lme4', 'recipes'

Packages suggested but not available for checking: 'furrr', 'ggimage'

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.
func.constructRegressionFormula: no visible global function definition
  for ‘as.formula’
func.crossValidationAnalysis: no visible global function definition for
  ‘glm’
func.crossValidationAnalysis: no visible global function definition for
  ‘predict’
func.crossValidationAnalysis: no visible global function definition for
  ‘write.table’
func.externalValidationAnalysis: no visible global function definition
  for ‘predict’
func.externalValidationAnalysis: no visible global function definition
  for ‘write.table’
func.linearRegressionAnalysis: no visible global function definition
  for ‘glm’
func.linearRegressionAnalysis: no visible global function definition
  for ‘predict’
func.linearRegressionAnalysis: no visible global function definition
  for ‘write.table’
func.sortDataColumns: no visible global function definition for
  ‘write.table’
mainfunc.q2: no visible global function definition for ‘write.table’
mainfunc.q2: no visible global function definition for ‘new’
mainfunc.stats: no visible global function definition for ‘write.table’
mainfunc.stats: no visible global function definition for ‘new’
Undefined global functions or variables:
  as.formula glm new predict write.table
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "as.formula", "glm", "predict")
  importFrom("utils", "write.table")
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/CVR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CVST.Rcheck/00install.out’ for details.
Packages required but not available: 'wavethresh', '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/cvTools.Rcheck/00install.out’ for details.
random.CV: no visible global function definition for ‘var’
regular.CV: 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: 'doParallel', 'glmnet'
Running examples in ‘cvwrapr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: computeError
> ### Title: Compute CV statistics from a prediction matrix
> ### Aliases: computeError
> 
> ### ** Examples
> 
> set.seed(1)
> x <- matrix(rnorm(500), nrow = 50)
> y <- rnorm(50)
> cv_fit <- kfoldcv(x, y, train_fun = glmnet::glmnet,
+                   predict_fun = predict, keep = TRUE)
Error in loadNamespace(x) : there is no package called ‘glmnet’
Calls: kfoldcv ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(cvwrapr)
  > 
  > test_check("cvwrapr")
  Error in library(glmnet) : there is no package called 'glmnet'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘computeError.Rmd’ using rmarkdown
Quitting from lines 32-42 (computeError.Rmd) 
Error: processing vignette ‘computeError.Rmd’ failed with diagnostics:
there is no package called 'glmnet'
--- failed re-building ‘computeError.Rmd’

--- re-building ‘kfoldcv.Rmd’ using rmarkdown
Quitting from lines 37-40 (kfoldcv.Rmd) 
Error: processing vignette ‘kfoldcv.Rmd’ failed with diagnostics:
there is no package called 'glmnet'
--- failed re-building ‘kfoldcv.Rmd’

SUMMARY: processing the following files failed:
  ‘computeError.Rmd’ ‘kfoldcv.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'bit64', 'Rmpfr'

Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc', 'Rglpk'

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

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

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

--- re-building ‘vignette.Rmd’ using rmarkdown
... adding corpus positions to table 'metadata'
Creating new corpus 'UNGA'
... encoding p-attribute 'word'
... writing tokenstream to disk (directly from R, equivalent to cwb-encode)
... creating indices (in memory)
... writing file: word.corpus
... writing file: word.lexicon
... writing file: word.lexicon.idx
... creating data for new registry file
... writing registry file
Creating new corpus 'AUSTEN'
... encoding p-attribute 'word'
... writing tokenstream to disk (directly from R, equivalent to cwb-encode)
... creating indices (in memory)
... writing file: word.corpus
... writing file: word.lexicon
... writing file: word.lexicon.idx
... creating data for new registry file
... writing registry file
... encoding p-attribute 'stem'
... encoding s-attribute 'book'
Quitting from lines 259-262 (vignette.Rmd) 
Error: processing vignette ‘vignette.Rmd’ failed with diagnostics:
there is no package called 'tm'
--- failed re-building ‘vignette.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘hydroPSO’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cxxfunplus.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'changepoint', 'raster', 'leaflet'
Running examples in ‘cycleRtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: interval_detect
> ### Title: Detect Intervals in a Ride.
> ### Aliases: interval_detect
> 
> ### ** Examples
> 
> data(intervaldata)
> 
> ## "intervaldata" is a ride that includes two efforts (2 & 5 minutes) and a cafe
> ## stop. The efforts are marked in the lap column, which we can use as a
> ## criterion.
> 
> with(intervaldata, tapply(X = delta.t, INDEX = lap, sum)) / 60  # Minutes.
        1         2         3         4         5 
45.566667  5.016667 90.483333  2.016667  8.750000 
> 
> ## The above shows the efforts were laps two and four. What was the power?
> with(intervaldata, tapply(X = power.W, INDEX = lap, mean))[c(2, 4)]
       2        4 
359.3256 424.5620 
> 
> ## And for the sake of example, some other summary metrics...
> l <- split(intervaldata, intervaldata$lap)
> names(l) <- paste("Lap", names(l))  # Pretty names.
> vapply(l, FUN.VALUE = numeric(3), FUN = function(x)
+   c(t.min = ride_time(x$timer.s) / 60, NP = NP(x), TSS = TSS(x)))
          Lap 1      Lap 2     Lap 3      Lap 4      Lap 5
t.min  45.23333   5.016667  53.50000   2.016667   8.600000
NP    223.50911 366.241091 189.25471 408.128994 141.569889
TSS    39.18992  11.670105  33.23323   5.825784   2.989273
> 
> ## Could we have gotten the same information without the lap column?
> ## Two efforts and a cafe stop == 7 sections.
> interval_detect(intervaldata, sections = 7, plot = TRUE)
Error in loadNamespace(x) : there is no package called ‘changepoint’
Calls: interval_detect -> interval_detect.cycleRdata
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cycling_data_analysis.Rmd’ using rmarkdown
Quitting from lines 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette ‘cycling_data_analysis.Rmd’ failed with diagnostics:
there is no package called 'leaflet'
--- failed re-building ‘cycling_data_analysis.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Andromeda', 'bit64'

Package suggested but not available for checking: ‘cmprsk’

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.
Packages required but not available: 'GoFKernel', 'viridis', 'plotly'

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cystiSim.Rcheck/00install.out’ for details.
Package required but not available: ‘jose’

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

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

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

Package suggested but not available for checking: ‘viridis’

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

Packages suggested but not available for checking: 'readr', '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.
Package required but not available: ‘readr’

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

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.
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/d3plus.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/d3po.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘partykit’
Package suggested but not available for checking: ‘DAAG’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DAAGbio.Rcheck/00install.out’ for details.
Package required but not available: ‘latticeExtra’

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

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

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

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/dae.Rcheck/00install.out’ for details.
Package required but not available: ‘FrF2’

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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dafs.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggdag’
Running examples in ‘dagwood-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dagwood
> ### Title: DAGs with Omitted Objects Displayed (DAGWOOD)
> ### Aliases: dagwood
> ### Keywords: DAG DAGWOOD causal inference
> 
> ### ** Examples
> 
> 
> # Generate a DAGWOOD from an example root DAG:
> DAG.root <-"Chocolate -> Alzheimers
+ Chocolate <- Education -> Alzheimers
+ Chocolate -> CV
+ CV -> Alzheimers"
> 
> # Identify the exposure and outcome of interest
> exposure <- "Chocolate"
> outcome <- "Alzheimers"
> 
> # Run the DAGWOOD algorithm and store results
> choc.alz.dagwood <- dagwood(DAG.root,exposure,outcome)
DAGWOOD has identified the following key assumptions, With respect to the root DAG:

. There are no common causes of both Alzheimers and CV that are not already adjusted- or controlled-for.
. There are no common causes of both Alzheimers and Chocolate that are not already adjusted- or controlled-for.
. There are no pathways through which CV causes Education except through nodes already accounted-for.
. There are no pathways through which Alzheimers can cause CV.
. There are no pathways through which both Alzheimers can cause Chocolate, and CV can cause Chocolate.
. There are no pathways through which CV can cause Chocolate.
. There are no pathways through which both Alzheimers can cause Education, and Chocolate can cause Education.
. There are no pathways through which Chocolate can cause Education.> 
> # Get the branch DAGs from the DAGWOOD object
> branch.DAGs <- choc.alz.dagwood$DAGs.branch
> 
> # Display the first branch DAG in the list
> library(ggdag)
Error in library(ggdag) : there is no package called ‘ggdag’
Execution halted
Package required but not available: ‘readr’

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

Package suggested but not available for checking: ‘phytools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DAKS.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'auditor', 'ggrepel', 'iml', 'lime', 'localModel', 'mlr', 'mlr3',
  'recipes', 'stacks', 'tidymodels'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DALEXtra.Rcheck/00install.out’ for details.
Packages required but not available: 'ggmcmc', 'dglm'

Packages suggested but not available for checking: 'rjags', 'dclone'

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:
  'car', 'effects', 'optiscale', 'AICcmodavg', 'latticeExtra', 'haven',
  'survey', 'srvyr'

Package suggested but not available for checking: ‘rstan’

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

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: 'behavr', 'readr'

Packages suggested but not available for checking: 'ggetho', 'zeitgebr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mapproj’
Error(s) in re-building vignettes:
  ...
--- re-building ‘dams.Rmd’ using rmarkdown
Loading required package: dams
Loading required package: ggplot2
Loading required package: maps
Loading required package: mapproj
Quitting from lines 122-123 (dams.Rmd) 
Error: processing vignette ‘dams.Rmd’ failed with diagnostics:
The package `mapproj` is required for `coord_map()`
--- failed re-building ‘dams.Rmd’

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

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

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

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
'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: 'adegenet', 'klaR', 'plotly'

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 required but not available:
  'adegenet', 'vegan', 'PopGenReport', 'StAMPP', 'SNPRelate', 'fields',
  'raster'

Packages suggested but not available for checking:
  'HardyWeinberg', 'tidyverse', 'doParallel', 'dismo', 'pegas',
  'rgdal', 'leaflet.minicharts', 'leaflet', 'poppr', 'gdistance',
  'seqinr', 'vcfR', 'mmod', 'plotly', 'ggrepel', 'ggtern', 'SIBER',
  'snpStats', 'hierfstat', 'gganimate', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
dashboard_open: no visible global function definition for ‘write.csv’
dashboard_open: no visible global function definition for
  ‘capture.output’
dctable: no visible global function definition for ‘capture.output’
Undefined global functions or variables:
  capture.output write.csv
Consider adding
  importFrom("utils", "capture.output", "write.csv")
to your NAMESPACE file.
Packages suggested but not available for checking: 'dash', 'plotly'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dash’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dash’
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dash’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'readr', 'bit64'

Packages suggested but not available for checking:
  'R.utils', 'RSQLite', 'Andromeda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'geometry', 'spdep', 'ProjectionBasedClustering', 'dendextend'
Package required but not available: ‘xlsx’

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: ‘devtools’
Package suggested but not available for checking: ‘bit64’
Packages required but not available: 'Hmisc', 'haven'

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: 'caret', 'GA'

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

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

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.
Package required but not available: ‘gsubfn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘my new data set.rds’
Package required but not available: ‘rio’

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

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: ‘devtools’

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dataPreparation.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: 'ggpubr', 'lme4', 'R.devices'

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.
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘xts’
Package required but not available: ‘Rlabkey’

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: ‘xts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘styler’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/datastructures.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'extremis', 'spearmanCI', 'ROCnReg'
Packages suggested but not available for checking:
  'bit64', 'R.utils', 'xts', 'nanotime'
Found the following significant warnings:
  fread.c:1278:38: warning: the comparison will always evaluate as ‘false’ for the pointer operand in ‘nastr + 8’ must not be NULL [-Waddress]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/data.table.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'party', 'partykit', 'doParallel', 'DiagrammeR'
Running examples in ‘data.tree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.Node
> ### Title: Plot a graph, or get a graphviz dot representation of the tree
> ### Aliases: plot.Node ToDiagrammeRGraph SetNodeStyle SetEdgeStyle
> ###   SetGraphStyle GetDefaultTooltip
> 
> ### ** Examples
> 
> data(acme)
> SetGraphStyle(acme, rankdir = "TB")
> SetEdgeStyle(acme, arrowhead = "vee", color = "blue", penwidth = 2)
> #per default, Node style attributes will be inherited:
> SetNodeStyle(acme, style = "filled,rounded", shape = "box", fillcolor = "GreenYellow", 
+              fontname = "helvetica", tooltip = GetDefaultTooltip)
> SetNodeStyle(acme$IT, fillcolor = "LightBlue", penwidth = "5px")
> #inheritance can be avoided:
> SetNodeStyle(acme$Accounting, inherit = FALSE, fillcolor = "Thistle", 
+              fontcolor = "Firebrick", tooltip = "This is the accounting department")
> SetEdgeStyle(acme$Research$`New Labs`, 
+              color = "red", 
+              label = "Focus!", 
+              penwidth = 3, 
+              fontcolor = "red")
> #use Do to set style on specific nodes:
> Do(acme$leaves, function(node) SetNodeStyle(node, shape = "egg"))
> plot(acme)
Error in plot.Node(acme) : 
  Package "DiagrammeR" is required to plot a `data.tree::Node`object. Please install it.
Calls: plot -> plot.Node
Execution halted
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘haven’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggmap', 'rworldmap', 'choroplethr', 'vioplot', 'plotly', 'ggrepel'
Error(s) in re-building vignettes:
  ...
--- re-building ‘DataVisualizations.Rmd’ using rmarkdown
Quitting from lines 71-87 (DataVisualizations.Rmd) 
Error: processing vignette ‘DataVisualizations.Rmd’ failed with diagnostics:
there is no package called 'vioplot'
--- failed re-building ‘DataVisualizations.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DataViz.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'gamm4', 'lme4', 'rstanarm'
Packages required but not available: 'Hmisc', 'labelled', 'readr'

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

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.
Packages required but not available: 'labdsv', '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/dawai.Rcheck/00install.out’ for details.
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.
Package required but not available: ‘lme4’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
dbEmpLikeGOF: no visible global function definition for ‘runif’
dbEmpLikeGOF: no visible global function definition for ‘var’
dbEmpLikeGOF: no visible global function definition for ‘rnorm’
emplikeGOFinternal: no visible global function definition for ‘var’
getCutoff: no visible binding for global variable ‘unifCut’
getCutoff: no visible binding for global variable ‘normCut’
getCutoff: no visible global function definition for ‘lm’
getCutoff: no visible binding for global variable ‘distEqCut’
getPval: no visible binding for global variable ‘unifCut’
getPval: no visible binding for global variable ‘normCut’
getPval: no visible global function definition for ‘lm’
getPval: no visible binding for global variable ‘distEqCut’
helperPval: no visible global function definition for ‘lm’
returnCutoff: no visible global function definition for ‘quantile’
testfun2: no visible global function definition for ‘runif’
testfun2: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  distEqCut lm normCut quantile rnorm runif unifCut var
Consider adding
  importFrom("stats", "lm", "quantile", "rnorm", "runif", "var")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dbEmpLikeNorm.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DBfit.Rcheck/00install.out’ for details.
Package required but not available: ‘RSQLite’

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

Packages suggested but not available for checking:
  'RSQLite', 'duckdb', 'bigrquery'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DBI-package
> ### Title: DBI: R Database Interface
> ### Aliases: DBI DBI-package
> 
> ### ** Examples
> 
> RSQLite::SQLite()
Error in loadNamespace(x) : there is no package called ‘RSQLite’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages suggested but not available for checking:
  'dblog', 'devtools', 'RSQLite'
Running examples in ‘DBItest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: make_context
> ### Title: Test contexts
> ### Aliases: make_context set_default_context get_default_context
> 
> ### ** Examples
> 
> make_context(
+   new(
+     "DBIConnector",
+     .drv = RSQLite::SQLite(),
+     .conn_args = list(dbname = tempfile("DBItest", fileext = ".sqlite"))
+   ),
+   tweaks = tweaks(
+     constructor_relax_args = TRUE,
+     placeholder_pattern = c("?", "$1", "$name", ":name"),
+     date_cast = function(x) paste0("'", x, "'"),
+     time_cast = function(x) paste0("'", x, "'"),
+     timestamp_cast = function(x) paste0("'", x, "'"),
+     logical_return = function(x) as.integer(x),
+     date_typed = FALSE,
+     time_typed = FALSE,
+     timestamp_typed = FALSE
+   ),
+   default_skip = c("roundtrip_date", "roundtrip_timestamp")
+ )
Error in loadNamespace(x) : there is no package called ‘RSQLite’
Calls: make_context ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘DBItest.Rmd’ using rmarkdown
Quitting from lines 130-155 (DBItest.Rmd) 
Error: processing vignette ‘DBItest.Rmd’ failed with diagnostics:
there is no package called 'RSQLite'
--- failed re-building ‘DBItest.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'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 required but not available:
  'spatstat.core', 'spatstat.geom', 'spatstat.random'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'bit64', 'odbc', 'RMariaDB', 'RPostgres', 'RPostgreSQL', 'RSQLite'
Running examples in ‘dbplyr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: arrange.tbl_lazy
> ### Title: Arrange rows by column values
> ### Aliases: arrange.tbl_lazy
> 
> ### ** Examples
> 
> library(dplyr, warn.conflicts = FALSE)
> 
> db <- memdb_frame(a = c(3, 4, 1, 2), b = c(5, 1, 2, NA))
Error in (function (cond)  : 
  error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called ‘RSQLite’
Calls: memdb_frame ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: ‘GBJ’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'fpc', 'dendextend'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dbWebForms.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'RSQLite', 'RMariaDB', 'RMySQL', 'RPostgres', 'RPostgreSQL', 'odbc'
'LazyData' is specified without a 'data' directory
Running examples in ‘dbx-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dbxConnect
> ### Title: Create a database connection
> ### Aliases: dbxConnect
> 
> ### ** Examples
> 
> # SQLite
> db <- dbxConnect(adapter="sqlite", dbname=":memory:")
Error in requireLib("RSQLite") : Could not load adapter: RSQLite
Calls: dbxConnect -> findAdapter -> requireLib
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dbx)
  > 
  > test_check("dbx")
  [ FAIL 1 | WARN 0 | SKIP 8 | PASS 0 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (4)
  • odbc (3)
  • redshift (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-sqlite.R:3:1): (code run outside of `test_that()`) ──────────────
  Error in `requireLib("RSQLite")`: Could not load adapter: RSQLite
  Backtrace:
      ▆
   1. └─dbx::dbxConnect(adapter = "rsqlite", dbname = ":memory:") at test-sqlite.R:3:0
   2.   └─dbx:::findAdapter(adapter)
   3.     └─dbx:::requireLib("RSQLite")
  
  [ FAIL 1 | WARN 0 | SKIP 8 | PASS 0 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘c3net’

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

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

Package suggested but not available for checking: ‘Ecdat’

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

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

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

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: 'idefix', 'mlogit', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘LFC.d.jpeg’ ‘LFC.s.jpeg’ ‘TF_bridged_DCL.pdf’
  ‘TF_bridged_DCL_int.pdf’
Package required but not available: ‘dnet’

Package suggested but not available for checking: ‘doMC’

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

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

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

Package suggested but not available for checking: ‘R2WinBUGS’

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: 'spacetime', 'DCluster', 'xts', 'lme4'

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

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

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

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

Package suggested but not available for checking: ‘rjags’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: modify,ANY,modifier-method
> ### Title: Modify records in a tbl
> ### Aliases: modify,ANY,modifier-method
> 
> ### ** Examples
> 
> library(DBI)
> library(dcmodify)
> library(dcmodifydb)
> 
> # silly modification rules
> m <- modifier( if (cyl == 6)  gear <- 10
+              , gear[cyl == 4] <- 0  # this R syntax works too :-)
+              , if (gear == 3) cyl <- 2
+              )
> 
> # setting up a table in the database
> con <- dbConnect(RSQLite::SQLite())
Error in (function (cond)  : 
  error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called ‘RSQLite’
Calls: dbConnect ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: ‘seqinr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'doParallel', 'Rfast', 'Rfast2'

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: 'doParallel', 'plotly'

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.
Package suggested but not available for checking: ‘gtsummary’
Error(s) in re-building vignettes:
  ...
--- re-building ‘dca.Rmd’ using rmarkdown
Quitting from lines 19-21 (dca.Rmd) 
Error: processing vignette ‘dca.Rmd’ failed with diagnostics:
there is no package called 'gtsummary'
--- failed re-building ‘dca.Rmd’

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

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

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

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.
Package required but not available: ‘segmented’

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

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

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

Packages suggested but not available for checking:
  'WGCNA', 'Biostrings', 'ggfortify'

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 required but not available: ‘orthopolynom’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
ifft: no visible global function definition for ‘fft’
lines.deamer: no visible global function definition for ‘lines’
rlaplace: no visible global function definition for ‘runif’
Undefined global functions or variables:
  fft lines runif
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "fft", "runif")
to your NAMESPACE file.
Package required but not available: ‘plotly’

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.
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: ‘truncdist’

Packages suggested but not available for checking: 'devtools', '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
compare.relimp: no visible global function definition for ‘qchisq’
compare.relimp: no visible global function definition for ‘pchisq’
plot_transition: no visible global function definition for ‘dnorm’
plot_transition: no visible global function definition for ‘par’
plot_transition: no visible global function definition for ‘lines’
plot_transition: no visible global function definition for ‘plogis’
plot_transition: no visible global function definition for ‘axis’
plot_transition: no visible global function definition for ‘mtext’
relative.importance: no visible global function definition for ‘glm’
relative.importance: no visible global function definition for ‘sd’
relative.importance : tr.pr: no visible global function definition for
  ‘pnorm’
relative.importance: no visible global function definition for ‘vcov’
Undefined global functions or variables:
  axis dnorm glm lines mtext par pchisq plogis pnorm qchisq sd vcov
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par")
  importFrom("stats", "dnorm", "glm", "pchisq", "plogis", "pnorm",
             "qchisq", "sd", "vcov")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'chillR', 'msm', 'rriskDistributions'

Package suggested but not available for checking: ‘mc2d’

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:
  'AER', 'future.apply', 'Matching', 'betareg', 'biglm', 'gam',
  'DesignLibrary', 'coin'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DeclareDesign.Rcheck/00install.out’ for details.
Packages required but not available: 'PSF', 'forecast', 'tseries'

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

Packages suggested but not available for checking:
  'EMD', 'Rssa', 'astrochron', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'BSgenome', 'BSgenome.Hsapiens.UCSC.hg19', 'GenomeInfoDb'

Package suggested but not available for checking: ‘VariantAnnotation’

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: ‘Deducer’

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

Depends: includes the non-default packages:
  'Deducer', 'psych', 'GPArotation', 'mvnormtest', 'irr', 'klaR'
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: 'JGR', 'car', 'multcomp', 'effects'

Package suggested but not available for checking: ‘Hmisc’

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: 'Deducer', 'tm', 'wordcloud'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ada', 'caret'
Packages suggested but not available for checking: 'devtools', 'ggraph'
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [57s/87s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(deepdep)
  > 
  > test_check("deepdep")
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 20 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • Build's Bioconductor and R version mismatch makes performing test impossible (2)
  • On CRAN (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-plot.R:17:1): (code run outside of `test_that()`) ───────────────
  Error in `plot_dependencies.deepdep(dd_rlang)`: Missing necessary packages.
  Backtrace:
      ▆
   1. ├─vcr::use_cassette(...) at test-plot.R:17:0
   2. │ └─cassette$call_block(...)
   3. ├─deepdep::plot_dependencies(dd_rlang) at test-plot.R:19:2
   4. └─deepdep:::plot_dependencies.deepdep(dd_rlang)
  
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 20 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘treeClust’

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: ‘Rfast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
binary.state: no visible global function definition for ‘runif’
dbn.dnn.train: no visible global function definition for ‘runif’
dropout.mask: no visible global function definition for ‘runif’
nn.train: no visible global function definition for ‘runif’
rbm.train: no visible global function definition for ‘runif’
sae.dnn.train: no visible global function definition for ‘runif’
show.digit: no visible global function definition for ‘gray’
show.digit: no visible global function definition for ‘image’
Undefined global functions or variables:
  gray image runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image")
  importFrom("stats", "runif")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Biostrings', 'seqinr'

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

Packages suggested but not available for checking:
  'tidyverse', 'phytools', 'paleotree', 'dispRity'

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: ‘StableEstim’

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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rstan', 'seriation'

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

Package suggested but not available for checking: ‘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/deltaPlotR.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'fts', 'vegan', 'mlogit'

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
Found the following files/directories:
  ‘smd_table.docx’
Packages required but not available:
  'forecast', 'ftsa', 'rainbow', 'cobs', 'strucchange'

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

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

Packages suggested but not available for checking:
  'seriation', 'heatmaply', 'DendSer', 'fpc'

Package which this enhances 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/dendRoAnalyst.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DendroSync.Rcheck/00install.out’ for details.
Packages required but not available:
  'brnn', 'oce', 'plotly', 'Cubist', 'viridis', 'dplR'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'seriation', 'gapmap'
Error(s) in re-building vignettes:
  ...
--- re-building ‘example_figures.Rmd’ using rmarkdown
Quitting from lines 28-32 (example_figures.Rmd) 
Error: processing vignette ‘example_figures.Rmd’ failed with diagnostics:
there is no package called 'seriation'
--- failed re-building ‘example_figures.Rmd’

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

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

Package suggested but not available for checking: ‘missMDA’

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

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

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: ‘clime’

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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/depend.truncation.Rcheck/00install.out’ for details.
Packages required but not available: 'Hmisc', 'rms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rdonlp2’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/depmix.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'gamlss', 'gamlss.dist', 'Rdonlp2'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/depmixS4.Rcheck/00install.out’ for details.
Packages required but not available: 'raster', 'rgdal', 'rgeos'

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

Packages suggested but not available for checking: 'sn', 'xts', '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/depth.Rcheck/00install.out’ for details.
Package required but not available: ‘xts’

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

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.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'exact2x2', 'DescTools', 'haven', 'Hmisc'

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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/desctable.Rcheck/00install.out’ for details.
Package required but not available: ‘DescTools’

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

Packages suggested but not available for checking: 'RDCOMClient', '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: ‘FitAR’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
arrayUpdate : pairUpdate: no visible global function definition for
  ‘runif’
conditionUpdate: no visible global function definition for ‘runif’
designGG: no visible global function definition for ‘runif’
experimentDesignTable: no visible global function definition for
  ‘write.csv’
plotAllScores: no visible global function definition for ‘png’
plotAllScores: no visible global function definition for ‘par’
plotAllScores: no visible global function definition for ‘text’
plotAllScores: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off par png runif text write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par", "text")
  importFrom("stats", "runif")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘myDesignGGSAplot.png’ ‘myDesignGG_arrayDesign.csv’
  ‘myDesignGG_conditionDesign.csv’
Package required but not available: ‘DeclareDesign’

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

Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'

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

Packages suggested but not available for checking: 'lmerTest', 'afex'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/desire.Rcheck/00install.out’ for details.
fs.agreement.part: no visible global function definition for ‘as.dist’
fs.agreement.part: no visible global function definition for ‘cor’
fs.leave.k.out.combn: no visible global function definition for ‘sd’
fs.leave.k.out.sample: no visible global function definition for ‘sd’
fs.rd: no visible global function definition for ‘pchisq’
fs.selection: no visible global function definition for ‘p.adjust’
plot.FIT: no visible global function definition for ‘qchisq’
plot.FIT: no visible global function definition for ‘ppoints’
plot.FIT: no visible global function definition for ‘points’
plot.FIT: no visible global function definition for ‘abline’
plotJn: no visible global function definition for ‘points’
robust.distance.signed: no visible global function definition for
  ‘mahalanobis’
snowball: no visible global function definition for ‘is’
snowball: no visible global function definition for ‘median’
weight.sd: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  abline as.dist cor is mahalanobis median p.adjust pchisq points
  ppoints qchisq sd
Consider adding
  importFrom("graphics", "abline", "points")
  importFrom("methods", "is")
  importFrom("stats", "as.dist", "cor", "mahalanobis", "median",
             "p.adjust", "pchisq", "ppoints", "qchisq", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package suggested but not available for checking: ‘FME’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'dclone', 'dcmle'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/detect.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: ‘itertools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'AER', 'ROI.plugin.glpk', 'ROI.plugin.alabama'
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(detectseparation)
  > 
  > test_check("detectseparation")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 18 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-separator_lpSolveAPI.R:31:1): (code run outside of `test_that()`) ──
  Error in `nrow(settings)`: object 'settings' not found
  Backtrace:
      ▆
   1. └─base::nrow(settings) at test-separator_lpSolveAPI.R:31:0
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 18 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘separation.Rmd’ using rmarkdown
Quitting from lines 113-114 (separation.Rmd) 
Error: processing vignette ‘separation.Rmd’ failed with diagnostics:
'ROI.plugin.glpk' * must be installed for this functionality.
--- failed re-building ‘separation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/deTestSet.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DetMCD.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:
  'autothresholdr', 'doParallel', 'filesstrings', 'ijtiff'

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

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/Devore7.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/devtools.Rcheck/00install.out’ for details.
Packages required but not available: 'glmnet', 'DynTxRegime'

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

Packages suggested but not available for checking: 'sirt', 'MLCIRTwithin'

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

Package suggested but not available for checking: ‘mirt’

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

Package suggested but not available for checking: ‘latticeExtra’

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

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/dfexplore.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'AER', 'mlogit', 'plm'
Running examples in ‘dfidx-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dfidx
> ### Title: Data frames with indexes
> ### Aliases: dfidx
> 
> ### ** Examples
> 
> 
> data("TravelMode", package = "AER")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘AER’
Calls: data -> find.package
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dfidx.Rmd’ using rmarkdown

Attaching package: 'dfidx'

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

    filter

Quitting from lines 60-62 (dfidx.Rmd) 
Error: processing vignette ‘dfidx.Rmd’ failed with diagnostics:
there is no package called 'AER'
--- failed re-building ‘dfidx.Rmd’

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

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

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.
checkRd: (7) mtaBin_next.Rd:62: \item in \value must have non-empty label
Packages required but not available: 'dplR', 'ggpubr'

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: ‘rstan’

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

Package suggested but not available for checking: ‘car’

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

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

Packages suggested but not available for checking:
  'GOstats', 'org.Hs.eg.db', 'AnnotationDbi', 'MEGENA', 'doMC'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addItems
> ### Title: Add multiple data items
> ### Aliases: addItems
> 
> ### ** Examples
> 
> 
>    # Add normalize counts (DGEList) and log2CPM as additional "assay" items in the DGEobj
>    dgeObj  <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
>    dgeList <- edgeR::calcNormFactors(edgeR::DGEList(dgeObj$counts), method="TMM")
Error in loadNamespace(x) : there is no package called ‘edgeR’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'edgeR', 'sva'

Packages suggested but not available for checking: 'biomaRt', 'zFPKM'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
cvm.test : cvm.pval.disc: no visible global function definition for
  ‘integrate’
cvm.test : cvm.pval.disc: no visible global function definition for
  ‘dchisq’
cvm.test : cvm.pval.disc: no visible global function definition for
  ‘nlm’
cvm.test : cvm.stat.disc: no visible global function definition for
  ‘knots’
cvm.test : cvm.pval.disc.sim: no visible global function definition for
  ‘knots’
cvm.test : cvm.pval.disc.sim: no visible global function definition for
  ‘runif’
cvm.test: no visible global function definition for ‘is.stepfun’
cvm.test: no visible global function definition for ‘knots’
ks.test : exact.pval : ts.pval: no visible global function definition
  for ‘ecdf’
ks.test : sim.pval: no visible global function definition for ‘runif’
ks.test : sim.pval : getks: no visible global function definition for
  ‘ecdf’
ks.test: no visible global function definition for ‘is.stepfun’
ks.test: no visible global function definition for ‘knots’
ks.test: no visible global function definition for ‘ecdf’
Undefined global functions or variables:
  dchisq ecdf integrate is.stepfun knots nlm runif
Consider adding
  importFrom("stats", "dchisq", "ecdf", "integrate", "is.stepfun",
             "knots", "nlm", "runif")
to your NAMESPACE file.
Packages required but not available: 'lmtest', 'qgam', 'lme4'

Packages suggested but not available for checking:
  'mgcViz', 'spaMM', 'glmmTMB'

Packages which this enhances but not available for checking:
  'phyr', 'rstan', 'rjags', 'BayesianTools'

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

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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'forecast', 'future.apply'

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

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

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

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

Packages suggested but not available for checking: 'KrigInv', 'GPareto'

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

Packages suggested but not available for checking: 'blockcluster', 'poLCA'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
dichromat: no visible global function definition for ‘col2rgb’
dichromat: no visible global function definition for ‘predict’
dichromat: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  col2rgb predict rgb
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("stats", "predict")
to your NAMESPACE file.
le.pesquisa: no visible global function definition for ‘txtProgressBar’
le.pesquisa: no visible global function definition for ‘type.convert’
le.pesquisa: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar type.convert
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "type.convert")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DIconvex.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dictionaRy.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rsample', 'did', 'didimputation'

Package suggested but not available for checking: ‘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/DidacticBoost.Rcheck/00install.out’ for details.
Package required but not available: ‘doParallel’

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

Package suggested but not available for checking: ‘plm’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
L2eV: no visible binding for global variable ‘constants’
L2w: no visible binding for global variable ‘constants’
dielectric: no visible global function definition for ‘new’
dielectric2plot: no visible global function definition for ‘reshape’
eV2L: no visible binding for global variable ‘constants’
t2eV: no visible binding for global variable ‘constants’
Undefined global functions or variables:
  constants new reshape
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "reshape")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package required but not available: ‘rfishbase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mboost', '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/difconet.Rcheck/00install.out’ for details.
Packages required but not available: 'pcaMethods', '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/diffdepprop.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/diffee.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘diagram’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/diffEnrich.Rcheck/00install.out’ for details.
Packages required but not available: 'rgdal', '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/diffIRT.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'qlcMatrix', 'Hmisc', 'lsa', '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
Packages required but not available: 'expm', 'viridis'

Package suggested but not available for checking: ‘strex’

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

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

VignetteBuilder package required for checking but not installed: ‘R.rsp’
checkRd: (7) GQD.aic.Rd:30: \item in \value must have non-empty label
checkRd: (7) GQD.dic.Rd:30: \item in \value must have non-empty label
Skipping vignette re-building
Packages suggested but not available for checking: 'Quandl', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Skipping vignette re-building
Packages suggested but not available for checking: 'Quandl', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
checkRd: (7) JGQD.dic.Rd:30: \item in \value must have non-empty label
Errors in running code in vignettes:
when running code in ‘Part_1_Introduction.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?
when running code in ‘Part_2_Transition_Densities.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?
when running code in ‘Part_3_Bivariate_Diffusions.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘Part_1_Introduction.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘Part_2_Transition_Densities.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘Part_3_Bivariate_Diffusions.Rmd’ using ‘UTF-8’... failed to complete the test
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DiffXTables.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: ‘msm’

Package suggested but not available for checking: ‘ShinyItemAnalysis’

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

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

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

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:
  'Matrix.utils', 'SingleCellExperiment', 'SummarizedExperiment',
  'splatter', 'zinbwave', 'S4Vectors', 'edgeR', 'ggpubr'

Packages suggested but not available for checking:
  'DelayedArray', 'DelayedMatrixStats', 'HDF5Array'

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dils.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘bibliometrix’
Packages suggested but not available for checking: 'FactoMineR', 'ggrepel'
Running examples in ‘dimensio-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bootstrap
> ### Title: Partial Bootstrap Analysis
> ### Aliases: bootstrap bootstrap-method bootstrap,numeric-method
> ###   bootstrap,integer-method summary,BootstrapVector-method
> ###   bootstrap,CA-method bootstrap,PCA-method
> 
> ### ** Examples
> 
> library(ggrepel)
Error in library(ggrepel) : there is no package called ‘ggrepel’
Execution halted
Package required but not available: ‘hnp’

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 required but not available: ‘DRR’

Packages suggested but not available for checking:
  'NMF', 'cccd', 'lle', 'loe', 'vegan'

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

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: ‘CDM’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dina.Rcheck/00install.out’ for details.
Package required but not available: ‘Hmisc’

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

Package suggested but not available for checking: ‘edgeR’

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 required but not available: ‘DWDLargeR’

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: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bigstatsr', 'doParallel', 'Rfast', 'Rfast2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'alphahull', 'latticeExtra'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'plotly', 'calibrate'

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

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

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.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘rotasym’

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

Packages suggested but not available for checking: 'INLA', 'SpatialEpi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'SingleCellExperiment', 'TSCAN', 'NetIndices', 'fpc', 'rpart.plot',
  'AnnotationDbi', 'org.Hs.eg.db'

Package suggested but not available for checking: ‘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/discfrail.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘CircStats’

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

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

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

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

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: 'readr', 'tm'

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
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 ‘DiscreteFDR.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘DiscreteFDR.Rmd’ using ‘UTF-8’... failed to complete the test
Package suggested but not available for checking: ‘cvmdisc’
Running ‘testthat.R’ [5s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(discretefit)
  > library(dgof)
  
  Attaching package: 'dgof'
  
  The following object is masked from 'package:stats':
  
      ks.test
  
  > 
  > test_check("discretefit")
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 8 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-stats.R:70:3): cvm_gof statistic is equal to groupFit statistis (cvmdisc) ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'cvmdisc'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-stats.R:70:2
   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 1 | PASS 8 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DiscreteInverseWeibull.Rcheck/00install.out’ for details.
p.discrete.adjust : <anonymous>: no visible global function definition
  for ‘stepfun’
Undefined global functions or variables:
  stepfun
Consider adding
  importFrom("stats", "stepfun")
to your NAMESPACE file.
Package suggested but not available for checking: ‘coin’
'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/DiscreteWeibull.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
value: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  qchisq
Consider adding
  importFrom("stats", "qchisq")
to your NAMESPACE file.
Package suggested but not available for checking: ‘FactoMineR’
Malformed Description field: should contain one or more complete sentences.
Package required but not available: ‘dials’

Packages suggested but not available for checking:
  'earth', 'klaR', 'mda', 'sda'

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

Packages suggested but not available for checking: 'caret', 'Ecdat', 'pec'

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

--- re-building ‘modeling.Rmd’ using rmarkdown
Quitting from lines 210-211 (modeling.Rmd) 
Error: processing vignette ‘modeling.Rmd’ failed with diagnostics:
there is no package called 'raster'
--- failed re-building ‘modeling.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DisHet.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'future.apply', 'bit64', 'benchmarkme', 'arrow'

Packages suggested but not available for checking:
  'readr', 'biglm', 'biglmm', 'speedglm'

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mvp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/disordR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/disparityfilter.Rcheck/00install.out’ for details.
Rd file 'dualFlashlight.fn.Rd':
  \usage lines wider than 90 characters:
     dualFlashlight.fn(result.df, wellName = "WELL_USAGE", x.name = "mean", y.name = "ssmd", sampleName = "Sample", sampleColor = "black", c ... [TRUNCATED]

Rd file 'imageDesign.fn.Rd':
  \usage lines wider than 90 characters:
     imageDesign.fn(dataOnePlate.df, wellName = NA, rowName, colName, wells = NULL, colors = NULL, title = " ")

Rd file 'imageIntensity.fn.Rd':
  \usage lines wider than 90 characters:
     imageIntensity.fn(data.df, intensityName = NA, plateName = "BARCODE", wellName = "WELL_USAGE", rowName, colName, sampleName = "Sample", ... [TRUNCATED]

Rd file 'plateWellSeries.fn.Rd':
  \usage lines wider than 90 characters:
     plateWellSeries.fn(data.df, intensityName = NA, plateName = "BARCODE", wellName = "WELL_USAGE", rowName, colName, show.wellTypes = NULL ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘car’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'devtools', 'gghalves', 'furrr', 'doParallel'
Error(s) in re-building vignettes:
  ...
--- re-building ‘de-analysis.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: 'lubridate'

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

    date, intersect, setdiff, union

Quitting from lines 49-57 (de-analysis.Rmd) 
Error: processing vignette ‘de-analysis.Rmd’ failed with diagnostics:
there is no package called 'gghalves'
--- failed re-building ‘de-analysis.Rmd’

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

--- re-building ‘de-timeseries.Rmd’ using rmarkdown

Attaching package: 'purrr'

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

    accumulate, when

Warning: Removed 2 row(s) containing missing values (geom_path).
Warning: Removed 16 row(s) containing missing values (geom_path).
Warning: Removed 10 row(s) containing missing values (geom_path).
--- finished re-building ‘de-timeseries.Rmd’

--- re-building ‘getting-started.Rmd’ using rmarkdown
--- finished re-building ‘getting-started.Rmd’

SUMMARY: processing the following files failed:
  ‘de-analysis.Rmd’ ‘de-parallel.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'castor', 'Claddis', 'geometry', 'phangorn', 'phyclust', 'vegan'

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cut_probes
> ### Title: Cut probes
> ### Aliases: cut_probes
> 
> ### ** Examples
> 
> path <- tempdir()
> dir.create (path)
> # download and save as FASTA "Chlamydia pneumoniae B21 contig00001,
> # whole genome shotgun sequence" (GI = 737435910)
> if (!requireNamespace("rentrez", quietly = TRUE)) {
+ stop("Package \"rentrez\" needed for this function to work. Please install it.", call. = FALSE)}
> reference.string <- rentrez::entrez_fetch(db = "nucleotide", id = 737435910,
+                                          rettype="fasta")
> write( x= reference.string, file = paste0 (path, "/fasta"))
> probes <- cut_probes (ref.seq.from.file = TRUE, fasta.file = paste0(path, "/fasta"),
+                      delete.fasta = TRUE, start = 1000, stop = 1500,
+                      start.correction = FALSE, size = c(400, 500),
+                      delete.incomplete = FALSE,
+                      delete.identical = FALSE, give.probes.id = TRUE, mc.cores = 1)
Error: Package "seqinr" needed for this function to work. Please install it.
Execution halted
Package suggested but not available for checking: ‘vegan’
Error(s) in re-building vignettes:
  ...
--- re-building ‘dissCqN.Rmd’ using rmarkdown
Quitting from lines 23-31 (dissCqN.Rmd) 
Error: processing vignette ‘dissCqN.Rmd’ failed with diagnostics:
there is no package called 'vegan'
--- failed re-building ‘dissCqN.Rmd’

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

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

Packages suggested but not available for checking: 'Cubist', 'gam'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
densest: no visible global function definition for ‘weighted.mean’
diss: no visible global function definition for ‘cov’
neighbors: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov weighted.mean
Consider adding
  importFrom("stats", "cov", "weighted.mean")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'doParallel', 'doRNG', 'activity'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Distance.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'fasterize', 'spData', 'raster'
Running examples in ‘distanceto-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: distance_raster
> ### Title: Distance to raster
> ### Aliases: distance_raster
> 
> ### ** Examples
> 
> # Load sf
> library(sf)
Linking to GEOS 3.10.2, GDAL 3.4.2, PROJ 9.0.0; sf_use_s2() is TRUE
> 
> # Load nc data
> nc <- st_read(system.file("shapes/sids.shp", package="spData"))
Error: `dsn` must point to a source, not an empty string.
Execution halted
Running ‘tinytest.R’ [0s/0s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   tinytest::test_package("distanceto")
  + }
  
  test_distanceraster.R.........    0 tests    
  test_distanceraster.R.........    0 tests    Error in library(spData) : there is no package called 'spData'
  Calls: <Anonymous> ... run_test_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Quitting from lines 61-82 (intro.Rmd) 
Error: processing vignette ‘intro.Rmd’ failed with diagnostics:
`dsn` must point to a source, not an empty string.
--- failed re-building ‘intro.Rmd’

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

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

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/distcomp.Rcheck/00install.out’ for details.
'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 suggested but not available for checking: ‘DiagrammeR’
Package required but not available: ‘factoextra’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'GoFKernel', 'plotly'
Packages required but not available:
  'distr', 'distrEx', 'distrSim', 'distrTEst', 'distrTeach', 'RandVar',
  'distrMod'

Package suggested but not available for checking: ‘Biobase’

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

Package suggested but not available for checking: ‘glogis’

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

Packages suggested but not available for checking: 'distrMod', 'distrTEst'

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

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.
Package required but not available: ‘GA’

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

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: 'distr', 'distrEx', 'RandVar'

Package suggested but not available for checking: ‘ismev’

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

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

Package suggested but not available for checking: ‘textir’

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: ‘distrEx’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/distr.Rcheck/00install.out’ for details.
Packages required but not available: 'distr', 'fBasics', 'fGarch'

Packages suggested but not available for checking: 'distrEx', 'distrMod'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘distr’

Package suggested but not available for checking: ‘distrEx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'distr', 'distrEx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘distrSim’

Package suggested but not available for checking: ‘distrEx’

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', 'RMariaDB', 'RPostgres', 'RPostgreSQL', 'RSQLite'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dittodb.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘vegan’
Packages required but not available: 'plotly', 'quantreg', 'uniReg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'FME', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggmulti', 'loon.ggplot', 'zenplots', 'loon.shiny', 'loon.tourr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘entropart’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/diverse.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'expm', 'caper', 'geiger'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/diversitree.Rcheck/00install.out’ for details.
Packages required but not available: 'ggpubr', 'rms', 'MapGAM', 'gam'

Package suggested but not available for checking: ‘BOLTSSIRR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'unmarked', 'glmulti', 'qpcR', 'raster', 'vegan'

Package suggested but not available for checking: ‘rgdal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qgraph’

Packages suggested but not available for checking:
  'xlsx', 'sendplot', 'HWxtest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/divo.Rcheck/00install.out’ for details.
Packages required but not available: 'tidyverse', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'splancs', 'spatstat.geom', 'spatstat'

Package suggested but not available for checking: ‘ecespa’

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.
Packages required but not available: 'Hmisc', 'RJDBC', 'RPostgres'

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 suggested but not available for checking: ‘httptest’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Workaround https://github.com/hadley/testthat/issues/144
  > Sys.setenv(R_TESTS="")
  > 
  > library(testthat)
  > library(httptest)
  Error in library(httptest) : there is no package called 'httptest'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting_started_with_dkanr.Rmd’ using rmarkdown
Quitting from lines 15-17 (getting_started_with_dkanr.Rmd) 
Error: processing vignette ‘getting_started_with_dkanr.Rmd’ failed with diagnostics:
there is no package called 'httptest'
--- failed re-building ‘getting_started_with_dkanr.Rmd’

SUMMARY: processing the following file failed:
  ‘getting_started_with_dkanr.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'nardl', 'dynlm', 'AER', 'lmtest', 'strucchange', 'wavethresh'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'expm', 'glmnet'

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: ‘MSEtool’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Packages required but not available: 'showtext', 'partykit'

Packages suggested but not available for checking:
  'forecast', 'funModeling', 'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'graph', 'Rgraphviz'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggrepel', 'MCMCpack'

Package suggested but not available for checking: ‘mcmcplots’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lmtest', '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/dml.Rcheck/00install.out’ for details.
Packages required but not available: 'raster', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nadiv’

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:
  'DiagrammeR', 'duckdb', 'odbc', 'RMariaDB', 'RPostgres', 'RSQLite',
  'tidyverse'
Package required but not available: ‘MCMCpack’

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: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'glmnet', 'ks'

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/dmt.Rcheck/00install.out’ for details.
Packages required but not available: 'xts', 'quantmod', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘multicool’

Package suggested but not available for checking: ‘testthis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'supraHex', 'graph', 'Rgraphviz'

Packages suggested but not available for checking: 'doParallel', 'Biobase'

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’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DNH4)
  > 
  > test_check("DNH4")
  Error in library(httptest) : there is no package called 'httptest'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Packages required but not available: 'spdep', 'GOstats'

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: 'ergm', 'sna', 'arm', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘MCMCpack’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DOBAD.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘OutliersO3’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘dobin.Rmd’ using rmarkdown
Quitting from lines 22-34 (dobin.Rmd) 
Error: processing vignette ‘dobin.Rmd’ failed with diagnostics:
Package OutliersO3 is needed for the vignette. Please install it.
--- failed re-building ‘dobin.Rmd’

SUMMARY: processing the following file failed:
  ‘dobin.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘pbkrtest’

Packages suggested but not available for checking: 'multcomp', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tm', 'glmnet', 'textstem'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘uwot’
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/docknitr.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘bit64’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘parsermd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
ppert: no visible global function definition for ‘pbeta’
prepare8pkg: no visible global function definition for ‘glob2rx’
qpert: no visible global function definition for ‘qbeta’
rpert: no visible global function definition for ‘rbeta’
Undefined global functions or variables:
  glob2rx pbeta qbeta rbeta
Consider adding
  importFrom("stats", "pbeta", "qbeta", "rbeta")
  importFrom("utils", "glob2rx")
to your NAMESPACE file.
Package suggested but not available for checking: ‘devtools’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package required but not available: ‘vcd’

Packages suggested but not available for checking: 'FrF2', 'DoE.wrapper'

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.
Package required but not available: ‘DoE.base’

Package which this enhances but not available for checking: ‘gurobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DoE.wrapper’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'FrF2', 'DoE.base'

Package suggested but not available for checking: ‘skpr’

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: 'doRNG', '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/doFuture.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/doMC.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'lme4', 'car', 'dynlm', 'betareg'
checkRd: (7) dominanceanalysis-package.Rd:98: invalid email address: clbustos_at_gmail_com
Package suggested but not available for checking: ‘RcmdrMisc’
checkRd: (7) rename.vars.Rd:37: invalid email address: macq\@llnl.gov.
Package suggested but not available for checking: ‘relaimpo’
checkRd: (7) domir-package.Rd:30: invalid email address: jluchman@gmail_com
Package required but not available: ‘arules’

Packages suggested but not available for checking:
  'censReg', 'CPE', 'ggpubr', 'Hmisc', 'timeROC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘itertools’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/doMPI.Rcheck/00install.out’ for details.
Package required but not available: ‘Morpho’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘caret’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/doParallel.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'readr', 'sqldf'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro.Rmd’ using rmarkdown
--- finished re-building ‘Intro.Rmd’

--- re-building ‘controlled.Rmd’ using rmarkdown
--- finished re-building ‘controlled.Rmd’

--- re-building ‘dea_scrape.Rmd’ using rmarkdown
--- finished re-building ‘dea_scrape.Rmd’

--- re-building ‘dea_street_names.Rmd’ using rmarkdown
--- finished re-building ‘dea_street_names.Rmd’

--- re-building ‘make_lookup_df.Rmd’ using rmarkdown
Quitting from lines 151-163 (make_lookup_df.Rmd) 
Error: processing vignette ‘make_lookup_df.Rmd’ failed with diagnostics:
there is no package called 'sqldf'
--- failed re-building ‘make_lookup_df.Rmd’

--- re-building ‘noslang_street_names.Rmd’ using rmarkdown
--- finished re-building ‘noslang_street_names.Rmd’

--- re-building ‘parse_lookup.Rmd’ using rmarkdown
Your search matched multiple categories. Please choose one 
from the following list and refine your search. Example: 
lookup_syn('mushrooms') or lookup_syn('psilocybin')
--- finished re-building ‘parse_lookup.Rmd’

SUMMARY: processing the following file failed:
  ‘make_lookup_df.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/doRedis.Rcheck/00install.out’ for details.
Packages required but not available: 'lme4', 'lmerTest'

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:
  'doParallel', 'doMPI', 'doRedis', 'devtools', 'pkgmaker'

Suggests orphaned package: ‘bibtex’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/doRNG.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'optmatch', 'DiPs'
Packages required but not available: 'DoseFinding', 'latticeExtra'

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/DoseFinding.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘caret’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/doSNOW.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘optmatch’
Package suggested but not available for checking: ‘rms’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dosresmeta.Rcheck/00install.out’ for details.
dostats: no visible binding for global variable ‘na.fail’
first: no visible global function definition for ‘head’
last: no visible global function definition for ‘tail’
pval.default: no visible global function definition for ‘.hasSlot’
pval.lm: no visible global function definition for ‘anova’
Undefined global functions or variables:
  .hasSlot anova head na.fail tail
Consider adding
  importFrom("methods", ".hasSlot")
  importFrom("stats", "anova", "na.fail")
  importFrom("utils", "head", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package suggested but not available for checking: ‘OpenMPController’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DoTC.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘dotdot.Rmd’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dotgen.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘myfile.ps’ ‘myfile.svg’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dotwhisker.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/DoubleCone.Rcheck/00install.out’ for details.
Packages required but not available:
  'mlr3', 'mlr3tuning', 'clusterGeneration', 'mlr3learners'

Packages suggested but not available for checking: 'glmnet', 'AER', 'bbotk'

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/DOVE.Rcheck/00install.out’ for details.
Package required but not available: ‘forecast’

Package suggested but not available for checking: ‘PerformanceAnalytics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘leaflet’
Package required but not available: ‘readr’

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 required but not available: 'raster', 'Rmpfr'

Packages suggested but not available for checking: 'rgeos', 'rgdal'

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:
  'alakazam', 'Biostrings', 'phangorn', 'shazam'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'tmvtnorm', 'CEoptim'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'exactci', 'ggpubr', 'raster'

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: ‘R.utils’

Packages suggested but not available for checking: 'Biobase', 'forecast'

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.
Packages suggested but not available for checking:
  'RMySQL', 'RPostgreSQL', 'RSQLite'
Packages required but not available: 'odbc', 'bit64'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rio’

Package suggested but not available for checking: ‘devtools’

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/DPP.Rcheck/00install.out’ for details.
Package required but not available: ‘Rmpfr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'Rmpfr', 'DPQmpfr'
Running examples in ‘DPQ-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: p1l1
> ### Title: Numerically Stable p1l1(t) = (t+1)*log(1+t) - t
> ### Aliases: p1l1 p1l1. p1l1p p1l1ser .p1l1ser
> 
> ### ** Examples
> 
> t <- seq(-1, 4, by=1/64)
> plot(t, p1l1ser(t, 1), type="l")
> lines(t, p1l1.(t), lwd=5, col=adjustcolor(1, 1/2)) # direct formula
> for(k in 2:6) lines(t, p1l1ser(t, k), col=k)
> 
> ## zoom in
> t <- 2^seq(-59,-1, by=1/4)
> t <- c(-rev(t), 0, t)
> stopifnot(!is.unsorted(t))
> k.s <- 1:12; names(k.s) <- paste0("k=", 1:12)
> 
> ## True function values: use Rmpfr with 256 bits precision: ---
> ### eventually move this to ../tests/ & ../vignettes/log1pmx-etc.Rnw
> #### FIXME: eventually replace with  if(requireNamespace("Rmpfr")){ ......}
> #### =====
> if((needRmpfr <- is.na(match("Rmpfr", (srch0 <- search())))))
+     require("Rmpfr")
Loading required package: Rmpfr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Rmpfr’
> p1l1.T <- p1l1.(mpfr(t, 256)) # "true" values
Error in mpfr(t, 256) : could not find function "mpfr"
Calls: p1l1.
Execution halted
Package required but not available: ‘MCMCpack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DIZutils', 'DQAstats'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DIZutils', 'future.apply'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'vroom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'drc', 'devtools'
Running examples in ‘dr4pl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: print.summary.dr4pl
> ### Title: Print the dr4pl object summary to screen.
> ### Aliases: print.summary.dr4pl
> 
> ### ** Examples
> 
> library(drc)  # Needed for the data set 'ryegras'
Error in library(drc) : there is no package called ‘drc’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dr4pl_derivatives.Rmd’ using rmarkdown
--- finished re-building ‘dr4pl_derivatives.Rmd’

--- re-building ‘walk_through_in_R.Rmd’ using rmarkdown
Quitting from lines 21-24 (walk_through_in_R.Rmd) 
Error: processing vignette ‘walk_through_in_R.Rmd’ failed with diagnostics:
there is no package called 'drc'
--- failed re-building ‘walk_through_in_R.Rmd’

SUMMARY: processing the following file failed:
  ‘walk_through_in_R.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'readr', 'ggforce'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dragulaR.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'disk.frame', 'ggraph', 'styler'
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘highcharter’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘drawBox.pdf’ ‘drawCircle.pdf’ ‘drawCurve.pdf’ ‘drawLine.pdf’
  ‘drawPoint.pdf’ ‘drawSettingsExample.pdf’ ‘drawText.pdf’ ‘export.pdf’
Package required but not available: ‘xlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rstan', 'sde'

Package suggested but not available for checking: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'multcomp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘SuperLearner’

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
Packages required but not available: 'drc', 'odbc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DiagrammeR’
GNU make is a SystemRequirements.
Packages required but not available:
  'maptools', 'raster', 'spatstat.geom', 'spatstat.core',
  'spatstat.linnet', 'spatstat', 'spdep'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dotwhisker', 'interplot', 'likert', 'tidyverse', 'car', 'arm'

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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'seqinr', 'doParallel', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'irlba'
Error(s) in re-building vignettes:
  ...
--- re-building ‘DrImpute.Rmd’ using rmarkdown
Quitting from lines 59-85 (DrImpute.Rmd) 
Error: processing vignette ‘DrImpute.Rmd’ failed with diagnostics:
there is no package called 'irlba'
--- failed re-building ‘DrImpute.Rmd’

SUMMARY: processing the following file failed:
  ‘DrImpute.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'SmartEDA', 'mlr', 'iml'

Package suggested but not available for checking: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'GenomicRanges', 'GenomeInfoDb', 'GenomicFeatures',
  'TxDb.Hsapiens.UCSC.hg19.knownGene', 'S4Vectors', 'org.Hs.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'DESeq2', 'SummarizedExperiment'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
compute_xsq: no visible global function definition for ‘chisq.test’
Undefined global functions or variables:
  chisq.test
Consider adding
  importFrom("stats", "chisq.test")
to your NAMESPACE file.
Packages required but not available: 'gam', '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/dr.Rcheck/00install.out’ for details.
Package required but not available: ‘CVST’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'spatstat.geom', 'S4Vectors', 'Seurat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'SuperLearner', 'np', 'future.apply'

Package suggested but not available for checking: ‘gam’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MESS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sqldf', 'DescTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'GSVA', 'clusterProfiler'

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.
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.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Packages required but not available:
  'xts', 'tsoutliers', 'forecast', 'dygraphs', 'seastests'

Package suggested but not available for checking: ‘stR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
DSBayes: no visible global function definition for ‘qnorm’
DSBayes: no visible global function definition for ‘coef’
DSBayes: no visible global function definition for ‘vcov’
DSBayes : MLE: no visible global function definition for ‘qnorm’
DSBayes: no visible global function definition for ‘integrate’
DSBayes : qfunc.numer : <anonymous>: no visible global function
  definition for ‘dnorm’
DSBayes : ds.numer: no visible global function definition for
  ‘integrate’
DSBayes : lower: no visible global function definition for ‘qlogis’
DSBayes : lower: no visible global function definition for ‘integrate’
DSBayes : upper: no visible global function definition for ‘qlogis’
DSBayes : upper: no visible global function definition for ‘integrate’
DSBayes: no visible global function definition for ‘optimize’
DSBayes: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  coef dnorm integrate optimize qlogis qnorm uniroot vcov
Consider adding
  importFrom("stats", "coef", "dnorm", "integrate", "optimize", "qlogis",
             "qnorm", "uniroot", "vcov")
to your NAMESPACE file.
Packages suggested but not available for checking: 'lme4', 'sirt'
Error(s) in re-building vignettes:
  ...
--- re-building ‘start.Rmd’ using rmarkdown
Quitting from lines 288-290 (start.Rmd) 
Error: processing vignette ‘start.Rmd’ failed with diagnostics:
there is no package called 'lme4'
--- failed re-building ‘start.Rmd’

SUMMARY: processing the following file failed:
  ‘start.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘tfplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DSI.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘viridis’
Error(s) in re-building vignettes:
  ...
--- re-building ‘DSjobtracker.Rmd’ using rmarkdown

Attaching package: 'magrittr'

The following object is masked from 'package:tidyr':

    extract


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 76-108 (DSjobtracker.Rmd) 
Error: processing vignette ‘DSjobtracker.Rmd’ failed with diagnostics:
there is no package called 'viridis'
--- failed re-building ‘DSjobtracker.Rmd’

SUMMARY: processing the following file failed:
  ‘DSjobtracker.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dslice.Rcheck/00install.out’ for details.
Package required but not available: ‘DSI’

Package suggested but not available for checking: ‘resourcer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DSI’

Packages suggested but not available for checking:
  'dsBaseClient', 'metafor'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Distance’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dsm.Rcheck/00install.out’ for details.
Packages required but not available: 'opalr', 'DSI'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'exactci', 'asht'

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: ‘rgdal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'splancs', 'shapefiles', 'rgeos', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rtdists’

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 required but not available: ‘ppcor’

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: ‘Hmisc’

Packages suggested but not available for checking:
  'latticeExtra', 'widgetframe'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'tensorregress', 'WeightedCluster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DTComPair.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: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘aws’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
DTK.plot: no visible global function definition for ‘axis’
DTK.plot: no visible global function definition for ‘title’
DTK.plot: no visible global function definition for ‘lines’
DTK.plot: no visible global function definition for ‘points’
DTK.test: no visible binding for global variable ‘sd’
DTK.test: no visible global function definition for ‘qtukey’
TK.test: no visible global function definition for ‘TukeyHSD’
TK.test: no visible global function definition for ‘aov’
Undefined global functions or variables:
  TukeyHSD aov axis lines points qtukey sd title
Consider adding
  importFrom("graphics", "axis", "lines", "points", "title")
  importFrom("stats", "TukeyHSD", "aov", "qtukey", "sd")
to your NAMESPACE file.
Package required but not available: ‘diagram’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'party', 'evtree', 'partykit', 'caret'

Package suggested but not available for checking: ‘rpart.utils’

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/dtrSurv.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘dygraphs’
Packages required but not available: 'nanotime', 'bit64'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dtw', 'lsa'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dtw', 'flexclust', 'ggrepel'

Package suggested but not available for checking: ‘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/dtw.Rcheck/00install.out’ for details.
Packages required but not available: 'raster', 'rgdal', 'dtw', 'caret'

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dtw', 'lsa', 'DTWBI'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'haven', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'qlcMatrix', 'Seurat'

Package suggested but not available for checking: ‘hdf5r’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘arrow’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/duckdb.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'tidyverse', 'rstatix'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DunnettTests.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dupiR.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'pedtools', 'forrel', 'pedprobr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'survey', 'tab'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tsDyn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dygraphs', 'raster', 'rgdal'

Package suggested but not available for checking: ‘hydroGOF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DWDLargeR.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'raster', 'R.utils'
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dwdradar)
  > 
  > test_check("dwdradar")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 36 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-readRadarFile.R:23:1): readRadarFile works for RW @ GRIDBASE/hourly/radolan/recent/bin/onefile ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'R.utils'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-readRadarFile.R:23:0
   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 36 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'glmnet', 'hglasso'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'maxLik', 'DiscreteWeibull', 'Ecdat'

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.
Packages required but not available: 'hydroGOF', '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: ‘xts’

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:
  'raster', 'drc', 'fields', 'insol', 'doParallel'

Packages suggested but not available for checking:
  'eesim', 'gstat', 'rgeos', 'spatstat', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'timereg', 'biglm', 'R.rsp', 'speedglm'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dynamichazard.Rcheck/00install.out’ for details.
Packages required but not available: 'NatureSounds', 'viridis', 'gganimate'

Package suggested but not available for checking: ‘imager’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'rgeos'

Package suggested but not available for checking: ‘rgdal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘xts’

Packages suggested but not available for checking: 'raster', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'tgp', 'plgp'
Running examples in ‘dynaTree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sens.dynaTree
> ### Title: Monte Carlo Sensitivity Analysis for dynaTree Models
> ### Aliases: sens.dynaTree
> ### Keywords: methods htest
> 
> ### ** Examples
> 
> ## friedman data
> library(tgp)
Error in library(tgp) : there is no package called ‘tgp’
Execution halted
Package suggested but not available for checking: ‘devtools’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DynComm.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dyncomp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dynCorr.Rcheck/00install.out’ for details.
Packages required but not available: 'irlba', 'lmds'

Packages suggested but not available for checking: 'lle', 'smacof', 'uwot'

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: ‘dynwrap’

Package suggested but not available for checking: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggraph', 'ggrepel', 'GillespieSSA2', 'lmds', 'viridis'

Packages suggested but not available for checking:
  'dynwrap', 'R.rsp', 'Seurat', 'SingleCellExperiment',
  'SummarizedExperiment'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GetIntMod: no visible global function definition for ‘arima’
GetLikeDI: no visible global function definition for ‘arima’
GetLikeDI: no visible global function definition for ‘logLik’
GetPV: no visible global function definition for ‘optimize’
GetPV: no visible global function definition for ‘pchisq’
fitdi: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  arima logLik optimize pchisq
Consider adding
  importFrom("stats", "arima", "logLik", "optimize", "pchisq")
to your NAMESPACE file.
Packages required but not available: 'car', 'lmtest'

Packages suggested but not available for checking: 'strucchange', 'TSA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'plotly', 'rms'

Package suggested but not available for checking: ‘gam’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'dynfeature', 'dyndimred', 'dynwrap', 'GA', 'ggforce', 'ggraph',
  'ggrepel'

Package suggested but not available for checking: ‘uwot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mstate’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dynpred.Rcheck/00install.out’ for details.
'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:
  'MCMCpack', 'quantreg', 'tseries'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dyn.Rcheck/00install.out’ for details.
Packages required but not available: 'fda', '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/DynTxRegime.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘hdf5r’
Package required but not available: ‘readr’

Packages suggested but not available for checking: 'dyndimred', '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/DysPIA.Rcheck/00install.out’ for details.
Packages required but not available:
  'accelerometry', 'doParallel', 'doSNOW'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Packages required but not available: 'plotly', 'R.utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'msm', 'hdi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'leaflet', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'betareg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘EpiEstim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tgp', 'tseries', 'fields', 'lmtest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotmo’

Packages suggested but not available for checking: 'gam', 'mda'

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: ‘abc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggalluvial', 'recipes'

Packages suggested but not available for checking:
  'parcats', 'earth', 'furrr', 'caret', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidycensus’

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/easycsv.Rcheck/00install.out’ for details.
Packages required but not available:
  'multiCA', 'rcompanion', 'FSA', 'fitdistrplus'

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: 'PMCMRplus', 'multcomp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'annotate', 'Biobase', 'diffcoexp', 'geneExpressionFromGEO',
  'GEOquery', 'jetset', 'R.utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

Packages suggested but not available for checking:
  'AnnotationDbi', '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/EasyMx.Rcheck/00install.out’ for details.
Package required but not available: ‘ClimProjDiags’

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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/easyPSID.Rcheck/00install.out’ for details.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'SSBtools', 'sdcTable'

Package suggested but not available for checking: ‘RegSDC’

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', 'verification'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/easyVerification.Rcheck/00install.out’ for details.
Package required but not available: ‘Rglpk’

Package which this enhances but not available for checking: ‘gurobi’

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: 'eatDB', 'haven'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggparty', 'partykit', '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:
  'survey', 'BIFIEsurvey', 'Hmisc', 'car', 'miceadds', 'EffectLiteR',
  'eatGADS', 'msm', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
eb: no visible global function definition for ‘optimize’
ebalance: no visible global function definition for ‘var’
Undefined global functions or variables:
  optimize var
Consider adding
  importFrom("stats", "optimize", "var")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘my-vignette.Rmd’
Package required but not available: ‘wavethresh’

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.
Package suggested but not available for checking: ‘GeneNet’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ebdbNet.Rcheck/00install.out’ for details.
Packages required but not available:
  'fasterize', 'raster', 'rgdal', 'RSQLite'

Package suggested but not available for checking: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'separationplot', 'Hmisc'

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.
Package required but not available: ‘mstate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ashr', 'mixsqp'

Package suggested but not available for checking: ‘REBayes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/EBPRS.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/ebreg.Rcheck/00install.out’ for details.
ebSNP: no visible global function definition for ‘optim’
Undefined global functions or variables:
  optim
Consider adding
  importFrom("stats", "optim")
to your NAMESPACE file.
Package required but not available: ‘drc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Ecfun’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rmpfr', 'xts', 'RSQLite'

Packages suggested but not available for checking: 'ghyp', 'fOptions'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatstat', 'spatstat.geom', 'spatstat.core', 'spatstat.random'

Package suggested but not available for checking: ‘dixon’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fda', 'BMA'

Packages suggested but not available for checking:
  'car', 'DescTools', 'Ecdat', 'ipumsr', 'fitdistrplus'

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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘leaflet’
Package suggested but not available for checking: ‘spData’
Running examples in ‘echelon-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: echebin
> ### Title: Echelon spatial scan statistic based on Binomial model
> ### Aliases: echebin
> ### Keywords: echelon analysis spatial scan statistic spatial cluster
> ###   deteciotn
> 
> ### ** Examples
> 
> ##Hotspot detection for non-white birth of North Carolina using echelon scan
> 
> #Non-white birth from 1974 to 1984 (case data)
> library(spData)
Error in library(spData) : there is no package called ‘spData’
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘readr’

Packages suggested but not available for checking:
  'ggrepel', 'ggspatial', 'httptest', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'geouy', 'haven', 'labelled', 'srvyr', 'survey'

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.
Packages required but not available: 'caret', 'WGCNA'

Packages suggested but not available for checking:
  'earth', 'factoextra', 'ComplexHeatmap', 'viridis', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'lmtest', 'earth'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘raster’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘ads_vignette.Rmd’ using rmarkdown
Quitting from lines 13-22 (ads_vignette.Rmd) 
Error: processing vignette ‘ads_vignette.Rmd’ failed with diagnostics:
there is no package called 'raster'
--- failed re-building ‘ads_vignette.Rmd’

--- re-building ‘advanced_vignette.Rmd’ using rmarkdown
Warning: The closing backticks on line 69 ("````") in advanced_vignette.Rmd do not match the opening backticks "```" on line 54. You are recommended to fix either the opening or closing delimiter of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote).
Quitting from lines 13-25 (advanced_vignette.Rmd) 
Error: processing vignette ‘advanced_vignette.Rmd’ failed with diagnostics:
there is no package called 'raster'
--- failed re-building ‘advanced_vignette.Rmd’

--- re-building ‘cds_vignette.Rmd’ using rmarkdown
Quitting from lines 13-22 (cds_vignette.Rmd) 
Error: processing vignette ‘cds_vignette.Rmd’ failed with diagnostics:
there is no package called 'raster'
--- failed re-building ‘cds_vignette.Rmd’

--- re-building ‘webapi_vignette.Rmd’ using rmarkdown
Quitting from lines 13-26 (webapi_vignette.Rmd) 
Error: processing vignette ‘webapi_vignette.Rmd’ failed with diagnostics:
there is no package called 'raster'
--- failed re-building ‘webapi_vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘ads_vignette.Rmd’ ‘advanced_vignette.Rmd’ ‘cds_vignette.Rmd’
  ‘webapi_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'raster', 'rgdal', 'landscapemetrics', 'rasterDT', 'rasterVis'

Package suggested but not available for checking: ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘neonUtilities’

Packages suggested but not available for checking:
  'reader', 'taxize', 'ggrepel', 'maptools', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sna', 'betareg', 'doParallel'

Packages suggested but not available for checking: 'ggraph', 'labdsv'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rjags’

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/EcoHydRology.Rcheck/00install.out’ for details.
Package required but not available: ‘rgeos’

Packages suggested but not available for checking:
  'vegan', 'splancs', 'FD', 'picante', 'geoR', 'raster', 'alphahull'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘diagram’

Package suggested but not available for checking: ‘seacarb’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘abc’

Packages suggested but not available for checking:
  'changepoint', 'picante', '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: ‘ggraph’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'sna', '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.
Package suggested but not available for checking: ‘ggraph’
Error(s) in re-building vignettes:
  ...
--- re-building ‘economiccomplexity.Rmd’ using rmarkdown
   [[ suppressing 785 column names '0011', '0012', '0013' ... ]]
   [[ suppressing 785 column names '0011', '0012', '0013' ... ]]

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

computing product projection...
--------------------------------------------------
0 threshold...
0.05 threshold...
0.1 threshold...
0.15 threshold...
0.2 threshold...
0.25 threshold...
0.3 threshold...
0.35 threshold...
0.4 threshold...
0.45 threshold achieves the avg number of connections
computing product projection...
--------------------------------------------------
0 threshold...
0.05 threshold...
0.1 threshold...
0.15 threshold...
0.2 threshold...
0.25 threshold...
0.3 threshold...
0.35 threshold...
0.4 threshold...
0.45 threshold...
0.5 threshold...
0.55 threshold achieves the avg number of connections
Quitting from lines 122-144 (economiccomplexity.Rmd) 
Error: processing vignette ‘economiccomplexity.Rmd’ failed with diagnostics:
there is no package called 'ggraph'
--- failed re-building ‘economiccomplexity.Rmd’

SUMMARY: processing the following file failed:
  ‘economiccomplexity.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘bipartite’

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ecoCopula’

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ecosim.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Package required but not available: ‘FD’

Package suggested but not available for checking: ‘vegan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'adehabitatHR', 'adehabitatMA', 'biomod2', 'dismo', 'maptools',
  'raster', 'rms', 'doParallel', 'vegan', 'snowfall', 'ks', 'Hmisc'

Packages suggested but not available for checking:
  'rgdal', 'alphahull', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'qgraph', 'Rmisc', 'vegan', 'vegclust'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'Hmisc', 'readr'
Packages required but not available: 'RSQLite', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'vegclust', 'smacof', 'vegan', 'viridis'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ecotraj.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/EcoTroph.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ecoval.Rcheck/00install.out’ for details.
Packages required but not available: 'glmnet', 'CVXR', 'multiridge', 'JOPS'

Packages suggested but not available for checking:
  'expm', 'doParallel', 'ggraph'

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/ecp.Rcheck/00install.out’ for details.
Package required but not available: ‘smoof’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'vars'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'spatstat.geom', 'spatstat', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dae', 'lme4', 'pbkrtest', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'spdep', 'tmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/edcc.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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'R.utils', 'tm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'httptest', 'devtools'
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 ‘edgarWebR.Rmd’ using rmarkdown
Quitting from lines 17-26 (edgarWebR.Rmd) 
Error: processing vignette ‘edgarWebR.Rmd’ failed with diagnostics:
there is no package called 'httptest'
--- failed re-building ‘edgarWebR.Rmd’

--- re-building ‘parsing.Rmd’ using rmarkdown
Quitting from lines 16-22 (parsing.Rmd) 
Error: processing vignette ‘parsing.Rmd’ failed with diagnostics:
there is no package called 'httptest'
--- failed re-building ‘parsing.Rmd’

SUMMARY: processing the following files failed:
  ‘edgarWebR.Rmd’ ‘parsing.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘edgeR’

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/EDISON.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/editrules.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/edl.Rcheck/00install.out’ for details.
Package required but not available: ‘xts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'vegan', 'sdpt3r'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘distr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘opGMMassessment’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/edrGraphicalTools.Rcheck/00install.out’ for details.
Package required but not available: ‘rstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'haven', 'lme4', 'quantreg', 'WeMix', 'Dire'

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.
Package required but not available: ‘flexsurv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rgeos', 'plotly', 'rgdal'

Packages suggested but not available for checking:
  'maptools', 'GGally', 'readr', 'tidyverse', 'ggmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'rstanarm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
geteegdata: no visible global function definition for ‘untar’
geteegdata: no visible global function definition for ‘read.table’
geteegdata: no visible global function definition for ‘write.csv’
geteegdata: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  read.table untar write.csv write.table
Consider adding
  importFrom("utils", "read.table", "untar", "write.csv", "write.table")
to your NAMESPACE file.
Package required but not available: ‘bigsplines’

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.
Package required but not available: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'nnfor'

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 required but not available: ‘R.utils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'R.matlab', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arm', 'vcd', 'maptools'

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: ‘rifle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘EFAtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘PCovR’

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: 'doParallel', 'gstat'

Package suggested but not available for checking: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'pcalg', 'RBGL'

Package suggested but not available for checking: ‘qgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mcclust’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'survey', 'lavaan.survey', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'seqinr', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'afex', 'BayesFactor', 'brms', 'car', 'gamm4', 'lme4', 'lmerTest',
  'mediation', 'rms', 'rstanarm', 'tidymodels'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lme4', 'survey'

Packages suggested but not available for checking:
  'pbkrtest', 'poLCA', 'heplots', 'car', 'betareg', 'alr4', 'robustlmm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Packages suggested but not available for checking:
  'DIFlasso', 'DIFboost', 'VGAMdata'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/EffectStars.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ef.Rcheck/00install.out’ for details.
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/eFRED.Rcheck/00install.out’ for details.
Package required but not available: ‘party’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'qgraph', 'semPlot', 'NetworkToolbox', 'GGally', 'fitdistrplus',
  'ggpubr'

Packages suggested but not available for checking:
  'R.matlab', 'infutil', 'mirt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rstan’

Packages suggested but not available for checking:
  'eggCountsExtra', '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/egg.Rcheck/00install.out’ for details.
Packages required but not available: 'geoR', 'SpatialTools', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘srvyr’

Packages suggested but not available for checking: 'survey', 'haven'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘EGRET’

Package suggested but not available for checking: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'dataRetrieval', 'fields'

Packages suggested but not available for checking:
  'EGRETci', 'doParallel', 'zyp'

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: 'vegdata', 'vegan'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/eHOF.Rcheck/00install.out’ for details.
Packages required but not available: 'plotly', 'xts', 'viridis'

Package suggested but not available for checking: ‘devtools’

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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'GA', 'doSNOW'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'eiPack', 'ei', 'wru', 'doParallel', 'overlapping', 'leaflet'

Package suggested but not available for checking: ‘tigris’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
eiginv: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
boot_pr_comp: no visible global function definition for ‘cov’
boot_pr_comp: no visible global function definition for ‘quantile’
boot_pr_comp: no visible global function definition for ‘segments’
boot_pr_comp: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline cov quantile segments
Consider adding
  importFrom("graphics", "abline", "segments")
  importFrom("stats", "cov", "quantile")
to your NAMESPACE file.
Package required but not available: ‘quantreg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘msm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'eiPack', 'msm', 'tmvtnorm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'blme'

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: 'ggrepel', 'ggiraphExtra'

Package suggested but not available for checking: ‘lightgbm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ks', 'mapsf'

Package suggested but not available for checking: ‘ggspatial’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'seriation', 'dendextend', 'haven'

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: 'glmnet', 'cvTools', 'qgraph'

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/elasticnet.Rcheck/00install.out’ for details.
Packages required but not available: 'vroom', 'matchr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'PoisNor', 'wgeesel'

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/elec.strat.Rcheck/00install.out’ for details.
Packages required but not available: 'haven', '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 required but not available: ‘msm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'devtools', 'gnumeric', 'lmtest', 'reader', 'readODS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'furrr', 'slippymath'

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
Packages required but not available: 'quantreg', 'sqldf'

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ELISAtools.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘devtools’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rmpfr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ICSNP', 'doParallel', 'doRNG'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'emulator', 'calibrator'
Error(s) in re-building vignettes:
  ...
--- re-building ‘ellipticpaper.Rnw’ using Sweave

Attaching package: ‘elliptic’

The following objects are masked from ‘package:stats’:

    sd, sigma

The following object is masked from ‘package:base’:

    is.primitive

Loading required package: emulator
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘emulator’
Loading required package: calibrator
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘calibrator’

Error: processing vignette ‘ellipticpaper.Rnw’ failed with diagnostics:
 chunk 50 (label = bacco_flow) 
Error in p.eqn8.supp(theta = c(0, 1/2), D1 = D1.elliptic, D2 = D2.elliptic,  : 
  could not find function "p.eqn8.supp"

--- failed re-building ‘ellipticpaper.Rnw’

--- re-building ‘residuetheorem.Rnw’ using Sweave
--- finished re-building ‘residuetheorem.Rnw’

SUMMARY: processing the following file failed:
  ‘ellipticpaper.Rnw’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/elmNNRcpp.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘BAMMtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sna’

Package suggested but not available for checking: ‘aniDom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/elrm.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: ‘kinship2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'latticeExtra', 'xlsx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lmerTest', 'sjstats'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'showtext', 'Microsoft365R'
Package required but not available: ‘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: ‘move’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'recipes', 'rsample', 'uwot'

Packages suggested but not available for checking:
  'irlba', 'lme4', 'rstanarm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘uwot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘HelpersMG’

Packages suggested but not available for checking: 'car', 'gam'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘PPtree’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/EMCluster.Rcheck/00install.out’ for details.
Packages required but not available: 'EMD', 'nnfor', 'forecast'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘R2jags’
Packages required but not available:
  'HLMdiag', 'readODS', 'saeRobust', 'spdep'

Packages suggested but not available for checking:
  'R.rsp', 'simFrame', 'rgeos', 'maptools'

VignetteBuilder package required for checking but not installed: ‘R.rsp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  emd-rubner.c:810:20: warning: ‘minI’ is used uninitialized [-Wuninitialized]
  emd-rubner.c:810:26: warning: ‘minJ’ is used uninitialized [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/emdist.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: ‘EMD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/emg.Rcheck/00install.out’ for details.
Package required but not available: ‘maxLik’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gganimate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘MCMCpack’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/emIRT.Rcheck/00install.out’ for details.
Package required but not available: ‘raster’

Packages suggested but not available for checking:
  'osmar', 'eixport', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xts', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rdflib’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/eMLEloglin.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘taxadb’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/emme2.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'biglm', 'brms', 'car', 'mediation', 'multcomp', 'pbkrtest', 'lme4',
  'lmerTest'

Packages which this enhances but not available for checking:
  'CARBayes', 'coxme', 'MCMCglmm', 'MCMCpack', 'rstanarm', 'sommer'
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: ‘GGally’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/EMMIXSSL.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/EMMREML.Rcheck/00install.out’ for details.
Package required but not available: ‘showtext’

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: ‘Cyclops’
Error(s) in re-building vignettes:
  ...
--- re-building ‘EmpiricalCiCalibrationVignette.Rmd’ using rmarkdown
--- finished re-building ‘EmpiricalCiCalibrationVignette.Rmd’

--- re-building ‘EmpiricalMaxSprtCalibrationVignette.Rmd’ using rmarkdown
Quitting from lines 50-61 (EmpiricalMaxSprtCalibrationVignette.Rmd) 
Error: processing vignette ‘EmpiricalMaxSprtCalibrationVignette.Rmd’ failed with diagnostics:
there is no package called 'Cyclops'
--- failed re-building ‘EmpiricalMaxSprtCalibrationVignette.Rmd’

--- re-building ‘EmpiricalPCalibrationVignette.Rmd’ using rmarkdown
--- finished re-building ‘EmpiricalPCalibrationVignette.Rmd’

SUMMARY: processing the following file failed:
  ‘EmpiricalMaxSprtCalibrationVignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'DESeq2', 'GenomicRanges'

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/EMP.Rcheck/00install.out’ for details.
Package required but not available: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sampleSelection’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/emulator.Rcheck/00install.out’ for details.
Packages required but not available: 'wrassp', 'RSQLite', 'readr'

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 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: ‘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.
Package required but not available: ‘readr’

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/endorse.Rcheck/00install.out’ for details.
Packages required but not available: 'maxLik', '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/EnergyOnlineCPM.Rcheck/00install.out’ for details.
Packages required but not available:
  'raster', 'gdistance', 'rgdal', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'robustHD', '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/EngrExpt.Rcheck/00install.out’ for details.
Packages required but not available:
  'raster', 'dismo', 'doSNOW', 'doParallel', 'maxnet', 'glmnet',
  'rangeModelMetadata'

Packages suggested but not available for checking:
  'spocc', 'rasterVis', 'blockCV', 'devtools', 'latticeExtra',
  'ecospat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'raster', 'dismo', 'rgeos', 'ENMeval', 'spatstat.geom',
  'spatstat.random', 'ggpubr', 'rgdal'

Packages suggested but not available for checking:
  'hypervolume', 'leaflet', 'ecospat', 'caret', 'CalibratR', 'fields',
  'pdp', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (7) p300cbp.1000bp.Rd:18: \item in \describe must have non-empty label
checkRd: (7) p300cbp.1000bp.Rd:19: \item in \describe must have non-empty label
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checkRd: (7) p300cbp.200bp.Rd:18: \item in \describe must have non-empty label
checkRd: (7) p300cbp.200bp.Rd:19: \item in \describe must have non-empty label
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checkRd: (7) p300cbp.200bp.Rd:25-26: \item in \describe must have non-empty label
Package suggested but not available for checking: ‘brglm’

Package which this enhances but not available for checking: ‘betareg’
Error(s) in re-building vignettes:
  ...
--- re-building ‘GLMs.Rmd’ using rmarkdown
--- finished re-building ‘GLMs.Rmd’

--- re-building ‘bias.Rmd’ using rmarkdown
Quitting from lines 66-70 (bias.Rmd) 
Error: processing vignette ‘bias.Rmd’ failed with diagnostics:
there is no package called 'brglm'
--- failed re-building ‘bias.Rmd’

--- re-building ‘exponential_family.Rmd’ using rmarkdown
--- finished re-building ‘exponential_family.Rmd’

SUMMARY: processing the following file failed:
  ‘bias.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dendextend', 'seqinr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'glmnet', 'bartMachine'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fields’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ensembleBMA.Rcheck/00install.out’ for details.
Package required but not available: ‘EnsembleBase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ensembleBMA’

Package suggested but not available for checking: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘EnsembleBase’

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: 'EnsembleBase', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ensembleBMA', 'gamlss', 'ensembleMOS', 'glmx'
Package required but not available: ‘caret’

Package suggested but not available for checking: ‘ipred’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Biostrings', 'DECIPHER'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmnet’

Packages suggested but not available for checking: 'ggforce', '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: ‘RYoudaoTranslate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggpubr', 'vegan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
diffcv: no visible global function definition for ‘sd’
diffcvall: no visible global function definition for ‘sd’
diffcvall: no visible global function definition for ‘fligner.test’
diffcvall: no visible global function definition for ‘p.adjust’
diffcvpFK: no visible global function definition for ‘fligner.test’
diffcvpFK: no visible global function definition for ‘p.adjust’
diffexp: no visible global function definition for ‘var’
diffexp: no visible global function definition for ‘t.test’
diffexp: no visible global function definition for ‘p.adjust’
diffexp2: no visible global function definition for ‘var’
diffexp2: no visible global function definition for ‘t.test’
diffexp2: no visible global function definition for ‘p.adjust’
diffnsepperm: no visible global function definition for ‘p.adjust’
diffseall: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  fligner.test p.adjust sd t.test var
Consider adding
  importFrom("stats", "fligner.test", "p.adjust", "sd", "t.test", "var")
to your NAMESPACE file.
Package required but not available: ‘mixtools’

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: 'drc', 'lmtest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘changepoint’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fitdistrplus', 'sn'

Packages suggested but not available for checking: 'vegan', 'picante'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gstat', 'maptools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rdisop', 'mixtools'

Packages suggested but not available for checking:
  'xcms', 'MSnbase', '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/enviPick.Rcheck/00install.out’ for details.
Packages required but not available:
  'doFuture', 'doRNG', 'fields', 'raster', 'rgeos', 'sparr',
  'spatstat.geom'

Packages suggested but not available for checking:
  'R.rsp', 'spatstat.random'

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', 'palinsol', 'RSAGA'

Package suggested but not available for checking: ‘rgdal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'kSamples', 'fitdistrplus', 'truncdist'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘aster2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/EnvNicheR.Rcheck/00install.out’ for details.
Packages required but not available: 'phangorn', 'seqinr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'changepoint', 'ecp', 'ismev'

Package suggested but not available for checking: ‘openair’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Hmisc’
Packages required but not available: 'R.devices', 'plotly'

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/epade.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Net1-fromR.inp’
Packages required but not available: 'irlba', 'imager', 'tidyverse'

Packages suggested but not available for checking:
  'elasticnet', 'ggcorrplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'nls2', 'raster', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'timeROC'

Packages suggested but not available for checking: 'c060', '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:
  'expss', 'questionr', 'readr', 'tidyverse', 'leaflet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘threejs’

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/EpiCurve.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: 'rstan', 'rstanarm', 'lme4'

Package suggested but not available for checking: ‘EpiEstim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/epiDisplay.Rcheck/00install.out’ for details.
Packages required but not available: 'odbc', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'coarseDataTools', 'fitdistrplus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DescTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'epicontacts', 'leaflet', 'ggmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'devtools', 'styler'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/EpiILMCT.Rcheck/00install.out’ for details.
Package required but not available: ‘adaptMCMC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘epidict’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘EpiEstim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'fields', 'forecast', 'imputeTS', 'lme4', 'nlts', 'statnet'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/epimdr.Rcheck/00install.out’ for details.
Packages required but not available:
  'networkDynamic', 'tergm', 'doParallel', 'ergm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GA', 'vcfR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'future.apply', 'R.utils', 'rstan'

Packages suggested but not available for checking:
  'EpiSoon', 'forecastHybrid'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘cmprsk’

Packages suggested but not available for checking:
  'mstate', 'lme4', 'demography', 'popEpi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'rgdal', 'spData', 'spatstat', 'maptools', 'rgeos', 'mapproj',
  'tidyverse'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/epiR.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘episcan_1geno_cc.txt’ ‘episcan_1geno_quant.txt’
  ‘episcan_2geno_cc.txt’ ‘episcan_2geno_quant.txt’
Package required but not available: ‘ggdag’

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘surveillance’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/episplineDensity.Rcheck/00install.out’ for details.
Package required but not available: ‘tmvtnorm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘epiR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/EpistemicGameTheory.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'bit64', 'plotly', 'tidyverse'

Package suggested but not available for checking: ‘taskscheduleR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
FCIplot: no visible global function definition for ‘na.omit’
FCIplot: no visible global function definition for ‘tail’
FCIplot: no visible global function definition for ‘grid’
FCIplot: no visible global function definition for ‘polygon’
FCIplot: no visible global function definition for ‘rgb’
linpred: no visible global function definition for ‘lm’
mplott: no visible global function definition for ‘par’
mplott: no visible global function definition for ‘na.omit’
mplott: no visible global function definition for ‘lines’
mplott: no visible global function definition for ‘legend’
mplott: no visible global function definition for ‘grid’
plott: no visible global function definition for ‘lines’
plott: no visible global function definition for ‘par’
plott: no visible global function definition for ‘grid’
tsideplot: no visible global function definition for ‘par’
tsideplot: no visible global function definition for ‘axis’
tsideplot: no visible global function definition for ‘grid’
Undefined global functions or variables:
  axis grid legend lines lm na.omit par polygon rgb tail
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "polygon")
  importFrom("stats", "lm", "na.omit")
  importFrom("utils", "tail")
to your NAMESPACE file.
Package required but not available: ‘RSQLite’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'irr', 'elasticnet'

Package suggested but not available for checking: ‘graph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'TopKLists', 'VennDiagram'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'rgeos', 'maptools', 'flexclust', 'rgdal', 'leaflet',
  'leaflet.extras', 'nngeo'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'lme4'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘xslt’

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'eplusr', 'future.apply'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: '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/epxToR.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'ggiraphExtra', 'FSA', 'PMCMRplus'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/EQL.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/eqs2lavaan.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘semTools’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/equaltestMI.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: ‘mirt’

Packages suggested but not available for checking: 'ltm', 'sna'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘equateIRT’

Package suggested but not available for checking: ‘ltm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (7) presmoothing.Rd:108-109: \item in \value must have non-empty label
checkRd: (7) presmoothing.Rd:109-110: \item in \value must have non-empty label
checkRd: (7) presmoothing.Rd:110-112: \item in \value must have non-empty label
checkRd: (7) presmoothing.Rd:112-113: \item in \value must have non-empty label
checkRd: (7) presmoothing.Rd:113-115: \item in \value must have non-empty label
The following files contain a license that requires
distribution of original sources:
  ‘upgreek.sty’
Please ensure that you have complied with it.
Package required but not available: ‘broom.mixed’

Packages suggested but not available for checking:
  'forecast', 'lme4', 'gtsummary'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/EquiSurv.Rcheck/00install.out’ for details.
Package required but not available: ‘PairedData’

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/EQUIVNONINF.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘quantreg’

Packages suggested but not available for checking: 'R.rsp', 'mzR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/erboost.Rcheck/00install.out’ for details.
Packages required but not available: 'lmtest', 'systemfit', 'tseries'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ergm', 'btergm', 'sna'

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: ‘ergm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ergm', 'egor', 'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ergm’

Packages suggested but not available for checking: 'sna', 'lmtest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ergm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'latticeExtra', 'sna', 'latentnet', 'tergm', 'ergm.count',
  'ergm.userterms', 'networkDynamic'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ergm.Rcheck/00install.out’ for details.
Package required but not available: ‘ergm’

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/erpR.Rcheck/00install.out’ for details.
Packages required but not available: 'glmnet', 'plsVarSel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/errint.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘errorize.Rmd’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/errorlocate.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'CircStats', 'plotly', 'raster', 'rasterVis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
ESA: no visible binding for global variable ‘var’
plot.esabcv: no visible global function definition for ‘points’
plot.esabcv: no visible global function definition for ‘axis’
plot.esabcv: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis points title var
Consider adding
  importFrom("graphics", "axis", "points", "title")
  importFrom("stats", "var")
to your NAMESPACE file.
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readODS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘esreg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'trialr', 'DiagrammeR', 'viridis'

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:
  'leafem', 'leaflet', 'maptools', 'raster', 'tmap', 'viridis'
Package suggested but not available for checking: ‘graph’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ESEA.Rcheck/00install.out’ for details.
Packages required but not available: 'raster', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘smoots’

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’

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.
Package required but not available: ‘datamods’

Package suggested but not available for checking: ‘rio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
cv.ES: no visible binding for global variable ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
Package required but not available: ‘quantreg’

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: ‘haven’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyverse', 'plotly', 'rio', 'forecast'

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: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'brms', 'lme4', 'doParallel'

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: ‘qgraph’

Package suggested but not available for checking: ‘JGL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘autoimage’

Packages suggested but not available for checking: 'gamlss.dist', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'AER', 'ivpack', 'car'
Running examples in ‘estimatr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lh_robust
> ### Title: Linear Hypothesis for Ordinary Least Squares with Robust
> ###   Standard Errors
> ### Aliases: lh_robust
> 
> ### ** Examples
> 
> 
> library(fabricatr)
> dat <- fabricate(
+   N = 40,
+   y = rpois(N, lambda = 4),
+   x = rnorm(N),
+   z = rbinom(N, 1, prob = 0.4),
+   clusterID = sample(1:4, 40, replace = TRUE)
+ )
> 
> # Default variance estimator is HC2 robust standard errors
> lhro <- lh_robust(y ~ x + z, data = dat, linear_hypothesis = "z + 2x = 0")
Loading required namespace: car
Failed with error:  ‘there is no package called ‘car’’
Error in loadNamespace(x) : there is no package called ‘car’
Calls: lh_robust ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package suggested but not available for checking: ‘doParallel’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Testing-estimators-with-EstimDiagnostics.Rmd’ using rmarkdown
Quitting from lines 20-27 (Testing-estimators-with-EstimDiagnostics.Rmd) 
Error: processing vignette ‘Testing-estimators-with-EstimDiagnostics.Rmd’ failed with diagnostics:
there is no package called 'doParallel'
--- failed re-building ‘Testing-estimators-with-EstimDiagnostics.Rmd’

SUMMARY: processing the following file failed:
  ‘Testing-estimators-with-EstimDiagnostics.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/estimraw.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘PSCBS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘estoutstorage’
descsto: 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 required but not available: ‘gmm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
.Transition: no visible global function definition for ‘rnorm’
.Transition.DC: no visible global function definition for ‘runif’
Simu.Cond.HR: no visible global function definition for ‘rpois’
Simu.Cond.HR: no visible global function definition for ‘runif’
Simu.Cond.HR: no visible global function definition for ‘hist’
Simu.Cond.HR: no visible global function definition for ‘var’
Simu.HR: no visible global function definition for ‘rpois’
Simu.HR: no visible global function definition for ‘runif’
Simu.HR: no visible global function definition for ‘hist’
Simu.HR: no visible global function definition for ‘var’
Undefined global functions or variables:
  hist rnorm rpois runif var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "rnorm", "rpois", "runif", "var")
to your NAMESPACE file.
Package required but not available: ‘quantmod’

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: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mapdata', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'spatstat.geom', 'spatstat.core', 'spatstat.random', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'SimComp', 'multcomp', 'mratios'
Package required but not available: ‘Rmpfr’

Package suggested but not available for checking: ‘httptest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggalluvial’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geometry', 'SNPRelate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readr’

Packages suggested but not available for checking:
  'RSQLite', 'RPostgreSQL', 'RMySQL'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ff’

Packages suggested but not available for checking: 'RSQLite', 'RJDBC'

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: ‘xslt’

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: ‘readr’

Package suggested but not available for checking: ‘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/eurocordexr.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘readr’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/EurosarcBayes.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 suggested but not available for checking:
  'EMCluster', 'FRESA.CAD', 'NMF', 'uwot'
Running examples in ‘Evacluster-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EMCluster
> ### Title: Expectation Maximization Clustering
> ### Aliases: EMCluster
> 
> ### ** Examples
> 
> library(datasets)
> data(iris)
> 
> rndSamples <- sample(nrow(iris),100)
> trainData <- iris[rndSamples,]
> testData <- iris[-rndSamples,]
> 
> clsut <- EMCluster(trainData[,1:4],3)
Error in loadNamespace(x) : there is no package called ‘EMCluster’
Calls: EMCluster ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages required but not available: 'tfplot', 'dse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/evalITR.Rcheck/00install.out’ for details.
Packages required but not available:
  'agricolae', 'car', 'ggcorrplot', 'kSamples', 'vegan'

Packages suggested but not available for checking:
  'ccChooser', 'corehunter'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'metafor', 'MetaUtility'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Evapotranspiration.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘SpatialExtremes’
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 197-209 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
could not find function "rmaxstab"
--- 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: ‘R.utils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'EventDetectR', 'plotly'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'imputeTS', 'forecast'

Package suggested but not available for checking: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'prodlim', 'rio'
Running ‘testthat.R’ [7s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(eventglm)
  > 
  > test_check("eventglm")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 28 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-jackknife-agree.R:2:5): Jackknife agrees with prodlim ───────────
  <packageNotFoundError/error/condition>
  Error in `library(prodlim)`: there is no package called 'prodlim'
  Backtrace:
      ▆
   1. └─base::library(prodlim) at test-jackknife-agree.R:2:4
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 28 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘example-analysis.Rmd’ using rmarkdown
Quitting from lines 302-313 (example-analysis.Rmd) 
Error: processing vignette ‘example-analysis.Rmd’ failed with diagnostics:
there is no package called 'rio'
--- failed re-building ‘example-analysis.Rmd’

--- re-building ‘extenstions.Rmd’ using rmarkdown
--- finished re-building ‘extenstions.Rmd’

--- re-building ‘stata-sas-comparason.Rmd’ using rmarkdown
--- finished re-building ‘stata-sas-comparason.Rmd’

SUMMARY: processing the following file failed:
  ‘example-analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/event.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'glmnet', 'changepoint'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'tidyquant', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'fitdistrplus', 'gestate'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/eventTrack.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: 'rstan', 'rstanarm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'meta', 'Cyclops'

Package suggested but not available for checking: ‘sn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/evmix.Rcheck/00install.out’ for details.
Packages required but not available: 'seqinr', 'geiger', 'phytools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'vegan', 'expm', 'MCMCpack'

Package suggested but not available for checking: ‘doParallel’

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: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘geomorph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rrepast', 'RNetLogo'

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: ‘partykit’

Packages suggested but not available for checking: 'multcomp', 'party'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rjags', 'doParallel', 'doRNG'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
EW : PhiP : Phi: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
Package required but not available: ‘exactci’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
BinomialCIone: no visible global function definition for ‘na.omit’
PairedCIone: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/exactci.Rcheck/00install.out’ for details.
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.
Malformed Description field: should contain one or more complete sentences.
build.mcx.obj: no visible global function definition for ‘glm’
build.mcx.obj: no visible binding for global variable ‘poisson’
build.mcx.obj: no visible global function definition for ‘fitted’
cab: no visible global function definition for ‘rbinom’
cab: no visible global function definition for ‘runif’
mcexact: no visible global function definition for ‘update’
rounded.tprob: no visible global function definition for ‘pt’
simtable.cab: no visible global function definition for ‘rbinom’
simtable.cab: no visible global function definition for ‘runif’
Undefined global functions or variables:
  fitted glm poisson pt rbinom runif update
Consider adding
  importFrom("stats", "fitted", "glm", "poisson", "pt", "rbinom",
             "runif", "update")
to your NAMESPACE file.
Package suggested but not available for checking: ‘ExactData’
Packages required but not available: 'readr', 'strex', 'styler'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/exams2sakai.Rcheck/00install.out’ for details.
Packages required but not available: 'splancs', 'SpatialTools'

Package suggested but not available for checking: ‘spBayes’

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: ‘devtools’
Package suggested but not available for checking: ‘tidycensus’
Package suggested but not available for checking: ‘readr’
Running examples in ‘excluder-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: check_resolution
> ### Title: Check screen resolution
> ### Aliases: check_resolution
> 
> ### ** Examples
> 
> # Check for survey previews
> data(qualtrics_text)
> check_resolution(qualtrics_text)
Error in `dplyr::mutate()`:
! Problem while computing `width = readr::parse_number(.data$width)`.
Caused by error in `loadNamespace()`:
! there is no package called ‘readr’
Backtrace:
     ▆
  1. ├─excluder::check_resolution(qualtrics_text)
  2. │ ├─... %>% keep_marked_column(.data$exclusion_resolution, keep)
  3. │ └─excluder::mark_resolution(...)
  4. │   └─... %>% ...
  5. ├─excluder:::keep_marked_column(...)
  6. │ └─x %>% ...
  7. ├─dplyr::select(...)
  8. ├─dplyr::filter(., .data$exclusion_resolution == "resolution")
  9. ├─dplyr::filter(., .data$width < width_min | .data$height < height_min)
 10. ├─dplyr::mutate(., width = readr::parse_number(.data$width), height = readr::parse_number(.data$height))
 11. ├─dplyr:::mutate.data.frame(...)
 12. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
 13. │   ├─base::withCallingHandlers(...)
 14. │   └─mask$eval_all_mutate(quo)
 15. ├─base::loadNamespace(x)
 16. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
 17. │ │ └─base withOneRestart(expr, restarts[[1L]])
 18. │ │   └─base doWithOneRestart(return(expr), restart)
 19. │ └─base::stop(cond)
 20. └─dplyr `<fn>`(`<pckgNtFE>`)
 21.   └─rlang::abort(...)
Execution halted
Packages suggested but not available for checking: 'INLA', 'rgeos', 'rgdal'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/excursions.Rcheck/00install.out’ for details.
Packages required but not available: 'magic', 'brms'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'Biostrings', 'IRanges', 'Rsamtools', 'GenomicRanges',
  'GenomicAlignments'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘httptest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sybil', 'gage'

Package suggested but not available for checking: ‘Biobase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fields', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lmtest', 'plm', 'rio'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'orthopolynom', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RSQLite', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘smoof’
Packages required but not available: 'mboost', 'BayesX', '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/experiment.Rcheck/00install.out’ for details.
Packages required but not available: 'far', 'DoE.base'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'CORElearn', 'semiArtificial'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mediation', 'weights'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rpart.plot’

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:
  'FactoMineR', 'GDAtools', 'quanteda.textmodels'
Package suggested but not available for checking: ‘Rmpfr’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/expm.Rcheck/00install.out’ for details.
Packages required but not available:
  'repmis', 'SuperLearner', 'gam', '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/ExPosition.Rcheck/00install.out’ for details.
Packages required but not available: 'spdep', 'rgeos', '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: ‘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/expss.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
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/exsic.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'PerformanceAnalytics', 'truncdist'
Running examples in ‘ExtDist-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Beta
> ### Title: The Standard Beta Distribution.
> ### Aliases: Beta dBeta eBeta iBeta lBeta pBeta qBeta rBeta sBeta
> 
> ### ** Examples
> 
> # Parameter estimation for a distribution with known shape parameters
> x <- rBeta(n=500, params=list(shape1=2, shape2=2))
> est.par <- eBeta(x); est.par

Parameters for the Beta distribution. 
(found using the  MOM method.)

 Parameter  Type Estimate
    shape1 shape 2.072842
    shape2 shape 2.014862


> plot(est.par)
Error in loadNamespace(x) : 
  there is no package called ‘PerformanceAnalytics’
Calls: plot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Distributions-Beta.Rmd’ using rmarkdown
[WARNING] This document format requires a nonempty <title> element.
  Defaulting to 'Distributions-Beta.knit' as the title.
  To specify a title, use 'title' in metadata or --metadata title="...".
--- finished re-building ‘Distributions-Beta.Rmd’

--- re-building ‘Distributions-Normal.Rmd’ using rmarkdown
[WARNING] This document format requires a nonempty <title> element.
  Defaulting to 'Distributions-Normal.knit' as the title.
  To specify a title, use 'title' in metadata or --metadata title="...".
--- finished re-building ‘Distributions-Normal.Rmd’

--- re-building ‘Distributions.Rmd’ using rmarkdown
[WARNING] This document format requires a nonempty <title> element.
  Defaulting to 'Distributions.knit' as the title.
  To specify a title, use 'title' in metadata or --metadata title="...".
--- finished re-building ‘Distributions.Rmd’

--- re-building ‘ParaEst-and-DistSel-by-ExtDist.Rmd’ using rmarkdown

Attaching package: 'ExtDist'

The following object is masked from 'package:stats':

    BIC

Quitting from lines 91-92 (ParaEst-and-DistSel-by-ExtDist.Rmd) 
Error: processing vignette ‘ParaEst-and-DistSel-by-ExtDist.Rmd’ failed with diagnostics:
there is no package called 'PerformanceAnalytics'
--- failed re-building ‘ParaEst-and-DistSel-by-ExtDist.Rmd’

SUMMARY: processing the following file failed:
  ‘ParaEst-and-DistSel-by-ExtDist.Rmd’

Error: Vignette re-building failed.
Execution halted
'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/extfunnel.Rcheck/00install.out’ for details.
bars: no visible global function definition for ‘segments’
cv.binomial: no visible binding for global variable ‘var’
cv.binomial: no visible global function definition for ‘abline’
cv.normal: no visible binding for global variable ‘var’
cv.normal: no visible global function definition for ‘abline’
cv.poisson: no visible binding for global variable ‘var’
cv.poisson: no visible global function definition for ‘abline’
plot.extlasso: no visible global function definition for ‘matplot’
plot.extlasso: no visible global function definition for ‘axis’
Undefined global functions or variables:
  abline axis matplot segments var
Consider adding
  importFrom("graphics", "abline", "axis", "matplot", "segments")
  importFrom("stats", "var")
to your NAMESPACE file.
Packages required but not available: 'raster', 'rgdal', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'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/extraTrees.Rcheck/00install.out’ for details.
Packages required but not available: 'sn', 'CompRandFld', 'fda'

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: ‘gmm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tmvtnorm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fields’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/extRemes.Rcheck/00install.out’ for details.
Packages required but not available:
  'ismev', 'fExtremes', 'extRemes', 'Renext'

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.
Package required but not available: ‘emplik’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
bootstrapCMLE: no visible global function definition for ‘qweibull’
bootstrapCMLE: no visible binding for global variable ‘sd’
bootstrapCMLE: no visible global function definition for ‘quantile’
bootstrapCenWbMix: no visible binding for global variable ‘sd’
bootstrapCenWbMix: no visible global function definition for ‘quantile’
cenWeibullMLE: no visible global function definition for ‘sd’
expmx.p2.censor: no visible global function definition for ‘dweibull’
expmx.p2.censor: no visible global function definition for ‘pweibull’
genWbMixIni: no visible global function definition for ‘runif’
log.llh.p2.censor: no visible global function definition for ‘dweibull’
log.llh.p2.censor: no visible global function definition for ‘pweibull’
quanWbMix : t.fun: no visible global function definition for ‘pweibull’
quanWbMix: no visible global function definition for ‘uniroot’
quanWbMix.int : t.fun: no visible global function definition for
  ‘pweibull’
quanWbMix.int: no visible global function definition for ‘uniroot’
simWbMix: no visible global function definition for ‘rbinom’
simWbMix: no visible global function definition for ‘rweibull’
Undefined global functions or variables:
  dweibull pweibull quantile qweibull rbinom runif rweibull sd uniroot
Consider adding
  importFrom("stats", "dweibull", "pweibull", "quantile", "qweibull",
             "rbinom", "runif", "rweibull", "sd", "uniroot")
to your NAMESPACE file.
Packages required but not available: 'doRNG', 'doSNOW'

Package suggested but not available for checking: ‘exuberdata’

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.
Malformed Description field: should contain one or more complete sentences.
Rd file 'distance2point.Rd':
  \usage lines wider than 90 characters:
     distance2point(x, y, viewerDistance, viewerHeight, resolutionX, resolutionY, screenWidth, screenHeight)
  \examples lines wider than 100 characters:
     function( x, y, viewerDistance, viewerHeight, resolutionX, resolutionY, screenWidth, screenHeight ) {

Rd file 'subtendedAngle.Rd':
  \usage lines wider than 90 characters:
     subtendedAngle(x1, y1, x2, y2, viewerDistance = 58.74, viewerHeight = 4.55, resolutionX = 1280, resolutionY = 1024, screenWidth = 33.97 ... [TRUNCATED]
  \examples lines wider than 100 characters:
     function( x1, y1, x2, y2, viewerDistance=58.74, viewerHeight=4.55, resolutionX=1280, resolutionY=1024, screenWidth=33.97, screenHeight= ... [TRUNCATED]
         d1 <- distance2point(x1, y1, viewerDistance, viewerHeight, resolutionX, resolutionY, screenWidth, screenHeight)
         d2 <- distance2point(x2, y2, viewerDistance, viewerHeight, resolutionX, resolutionY, screenWidth, screenHeight)

These lines will be truncated in the PDF manual.
Package required but not available: ‘broom.mixed’

Packages suggested but not available for checking:
  'lme4', 'glmmTMB', 'doMC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/eyeTrackR.Rcheck/00install.out’ for details.
Package required but not available: ‘forestmodel’

Package suggested but not available for checking: ‘furrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘doSNOW’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘drc’

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.
Malformed Title field: should not end in a period.
Package required but not available: ‘R.utils’

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: 'haven', 'vroom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'car', 'lme4'

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.
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
createFormula: no visible global function definition for ‘tail’
createFormula: no visible global function definition for ‘head’
createFormula: no visible global function definition for ‘as.formula’
ezsim: no visible global function definition for ‘runif’
plot.ezsim: no visible global function definition for ‘quantile’
plot.ezsim: no visible global function definition for ‘head’
plot.ezsim: no visible global function definition for ‘tail’
plot.ezsim: no visible binding for global variable ‘dnorm’
plot.ezsim: no visible binding for global variable ‘pdf’
plot.ezsim: no visible global function definition for ‘dev.off’
plot.ezsim : <anonymous>: no visible global function definition for
  ‘dev.new’
plot.summary.ezsim: no visible global function definition for ‘head’
plot.summary.ezsim: no visible global function definition for ‘tail’
plot.summary.ezsim: no visible binding for global variable ‘pdf’
plot.summary.ezsim: no visible global function definition for ‘dev.off’
plot.summary.ezsim : <anonymous>: no visible global function definition
  for ‘dev.new’
Undefined global functions or variables:
  as.formula dev.new dev.off dnorm head pdf quantile runif tail
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("stats", "as.formula", "dnorm", "quantile", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Packages required but not available: 'ada', 'GA', 'glmnet'

Packages suggested but not available for checking: 'doParallel', 'rsample'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'NMF', 'doParallel', 'doRNG', 'pkgmaker'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ATAforecasting’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘prophet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'feasts', 'forecast'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fable.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'fable', 'future.apply', 'feasts'
Running examples in ‘fabletools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: features
> ### Title: Extract features from a dataset
> ### Aliases: features features_at features_all features_if
> 
> ### ** Examples
> 
> # Provide a set of functions as a named list to features.
> library(tsibble)

Attaching package: ‘tsibble’

The following objects are masked from ‘package:base’:

    intersect, setdiff, union

> tourism %>% 
+   features(Trips, features = list(mean = mean, sd = sd))
# A tibble: 304 × 5
   Region         State              Purpose    mean    sd
   <chr>          <chr>              <chr>     <dbl> <dbl>
 1 Adelaide       South Australia    Business 156.   35.6 
 2 Adelaide       South Australia    Holiday  157.   27.1 
 3 Adelaide       South Australia    Other     56.6  17.3 
 4 Adelaide       South Australia    Visiting 205.   32.5 
 5 Adelaide Hills South Australia    Business   2.66  4.30
 6 Adelaide Hills South Australia    Holiday   10.5   6.37
 7 Adelaide Hills South Australia    Other      1.40  1.65
 8 Adelaide Hills South Australia    Visiting  14.2  10.7 
 9 Alice Springs  Northern Territory Business  14.6   7.20
10 Alice Springs  Northern Territory Holiday   31.9  18.1 
# … with 294 more rows
> 
> # Search and use useful features with `feature_set()`. 
> 
> ## Don't show: 
> if (requireNamespace("feasts", quietly = TRUE)) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ library(feasts)
+ ## Don't show: 
+ }) # examplesIf
> ## End(Don't show)
> tourism %>% 
+   features(Trips, features = feature_set(tags = "autocorrelation"))
Error in .l[[1]] : subscript out of bounds
Calls: %>% ... features.tbl_ts -> features_impl -> map -> lapply -> FUN -> transpose
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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FacPad.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FactMixtAnalysis.Rcheck/00install.out’ for details.
Package required but not available: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'dendextend', 'FactoMineR', 'ggpubr', 'ggrepel'

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: 'car', 'ggrepel'

Packages suggested but not available for checking: 'missMDA', 'Factoshiny'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/factoptd.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FactorAssumptions.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FactorCopula.Rcheck/00install.out’ for details.
Packages required but not available:
  'arm', 'genlasso', 'prodlim', '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/factorial2x2.Rcheck/00install.out’ for details.
Packages required but not available: 'ggpubr', 'agricolae'

Package suggested but not available for checking: ‘survminer’

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.
Packages suggested but not available for checking:
  'relaimpo', 'lmtest', 'car', 'usdm', 'hier.part'
Package required but not available: ‘MCMCpack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'FactoMineR', 'FactoInvestigate', 'ggrepel', 'missMDA'

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: ‘factset.protobuf.stach.v2’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/factset.protobuf.stach.v2.Rcheck/00install.out’ for details.
Packages required but not available:
  'elasticnet', 'sparseLDA', 'sda', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'MFPCA', 'fda', 'fda.usc', 'funData'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fad.Rcheck/00install.out’ for details.
Package required but not available: ‘quantreg’

Package suggested but not available for checking: ‘ggraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'irr', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'optiSolve', 'CVXR', 'glmnet'

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 ‘Advanced_tutorial.Rmd’ using rmarkdown
Loaded gbm 2.1.8
Welcome to DALEX (version: 2.4.0).
Find examples and detailed introduction at: http://ema.drwhy.ai/
Additional features will be available after installation of: ggpubr.
Use 'install_dependencies()' to get all suggested dependencies
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Quitting from lines 230-245 (Advanced_tutorial.Rmd) 
Error: processing vignette ‘Advanced_tutorial.Rmd’ failed with diagnostics:
Package "ggrepel" needed for this function to work. Please install it.
--- failed re-building ‘Advanced_tutorial.Rmd’

--- re-building ‘Basic_tutorial.Rmd’ using rmarkdown
Warning in drop_metrics_with_na(data) :
  Found metric with NA: TNR, NPV, FNR, FOR, NEW_METRIC, omiting it

Quitting from lines 248-249 (Basic_tutorial.Rmd) 
Error: processing vignette ‘Basic_tutorial.Rmd’ failed with diagnostics:
Package "ggrepel" needed for this function to work. Please install it.
--- failed re-building ‘Basic_tutorial.Rmd’

SUMMARY: processing the following files failed:
  ‘Advanced_tutorial.Rmd’ ‘Basic_tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'caret', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
faisalconjoint: no visible global function definition for ‘barplot’
faisalconjoint: no visible global function definition for ‘text’
faisalconjoint: no visible global function definition for ‘jpeg’
faisalconjoint: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  barplot dev.off jpeg text
Consider adding
  importFrom("grDevices", "dev.off", "jpeg")
  importFrom("graphics", "barplot", "text")
to your NAMESPACE file.
Found the following files/directories:
  ‘FCMgraph.jpg’
Package suggested but not available for checking: ‘devtools’
Package vignette with placeholder title ‘Vignette Title’:
  ‘my-vignette.Rmd’
Packages required but not available: 'Familias', 'paramlink'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘fame/R/windows/zzz.R’:
  .onLoad calls:
    packageStartupMessage("FAME environment variable not set; assuming ",     defaultDir)
    packageStartupMessage("FAME directory ", fameDir, " not found.\n",     "If you have FAME installed, specify it's location ", "via the FAME environment variable.\n",     "Otherwise, this package is pretty useless.\n")

See section ‘Good practice’ in ‘?.onAttach’.
Packages required but not available: 'LipidMS', 'accucor'

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: ‘DepthProc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'BART', 'CORElearn', 'Ecdat', 'glmnet', 'harmonicmeanp', 'laGP',
  'mboost', 'partykit', 'randomForestSRC'
Packages required but not available: 'kinship2', 'paramlink'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
coef.FAMILY: no visible global function definition for ‘glm’
coef.FAMILY: no visible global function definition for ‘lm’
fm2v: no visible global function definition for ‘na.omit’
l_inf_prox: no visible global function definition for ‘tail’
predict.FAMILY: no visible global function definition for ‘coef’
predict.FAMILY: no visible global function definition for ‘lm’
predict.FAMILY: no visible global function definition for ‘predict’
predict.FAMILY: no visible global function definition for ‘glm’
predict.FAMILY: no visible global function definition for ‘predict.glm’
v2fm: no visible global function definition for ‘tail’
Undefined global functions or variables:
  coef glm lm na.omit predict predict.glm tail
Consider adding
  importFrom("stats", "coef", "glm", "lm", "na.omit", "predict",
             "predict.glm")
  importFrom("utils", "tail")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FAmle.Rcheck/00install.out’ for details.
Package required but not available: ‘R.utils’

Package suggested but not available for checking: ‘future.batchtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'kinship2', 'coxme'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FAMT.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fanc.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/fanovaGraph.Rcheck/00install.out’ for details.
Packages required but not available: 'sem', 'mirt'

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: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fBasics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/far.Rcheck/00install.out’ for details.
Packages required but not available: 'Benchmarking', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tidyverse’
Package required but not available: ‘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/fasjem.Rcheck/00install.out’ for details.
Packages required but not available:
  'timeSeries', 'fBasics', 'fMultivar', 'sn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fitdistrplus', 'tidyhydat', 'zyp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘LRMF3’

Package suggested but not available for checking: ‘invertiforms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggpubr’

Packages suggested but not available for checking: 'R.utils', 'viridis'

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/fastclime.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fastcmh.Rcheck/00install.out’ for details.
Package required but not available: ‘dynpred’

Packages suggested but not available for checking: 'cmprsk', 'crrp'

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 required but not available: ‘CUB’

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fastGHQuad.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fastglm.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FastHCS.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fastHICA.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘caret’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FastJM.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'coxKM', 'SKAT'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FastKM.Rcheck/00install.out’ for details.
Package required but not available: ‘fields’

Package suggested but not available for checking: ‘ngspatial’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'FactoClass'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘speedglm’
'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'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘fastmatch/libs/fastmatch.so’:
  Found non-API call to R: ‘match5’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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/FastPCS.Rcheck/00install.out’ for details.
'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: 'mosaic', 'maxLik'

Packages suggested but not available for checking:
  'ggformula', 'mosaicCalc', 'readr', 'faraway', 'Hmisc', 'DAAG',
  'multcomp', 'vcd', 'car', 'alr4', 'BradleyTerry2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FastRCS.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fastRG.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'furrr', 'ggrepel', 'RSQLite'
.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
Note: information on .o files is not available
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'earth', 'lightgbm'
Packages suggested but not available for checking:
  'xts', 'dygraphs', 'Rfast', 'Rfast2'
Error(s) in re-building vignettes:
  ...
--- re-building ‘fastverse_intro.Rmd’ using rmarkdown
Quitting from lines 64-72 (fastverse_intro.Rmd) 
Error: processing vignette ‘fastverse_intro.Rmd’ failed with diagnostics:
there is no package called 'xts'
--- failed re-building ‘fastverse_intro.Rmd’

SUMMARY: processing the following file failed:
  ‘fastverse_intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'kinship2', 'multgee'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lle’

Package suggested but not available for checking: ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘timeSeries’

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: ‘haven’
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fauxnaif)
  > 
  > test_check("fauxnaif")
  [ FAIL 1 | WARN 0 | SKIP 10 | PASS 34 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (10)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-na_if_in.R:126:3): with haven_labelled ──────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'haven'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-na_if_in.R:126:2
   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 10 | PASS 34 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘lme4’

Packages suggested but not available for checking:
  'broom.mixed', 'lmerTest', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'bvartools', 'MCMCpack', 'doParallel'

Package suggested but not available for checking: ‘vars’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FAwR.Rcheck/00install.out’ for details.
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/fbati.Rcheck/00install.out’ for details.
FBN.histogramMaxima: no visible global function definition for ‘hist’
FBN.kmeans: no visible global function definition for ‘median’
FBN.kmeans: no visible global function definition for ‘kmeans’
FBNormalization: no visible global function definition for ‘read.table’
FBNormalization: no visible global function definition for ‘median’
FBNormalization: no visible global function definition for ‘hist’
FBNormalization: no visible global function definition for ‘par’
FBNormalization: no visible global function definition for ‘dev.print’
FBNormalization: no visible binding for global variable ‘bmp’
FBNormalization: no visible global function definition for ‘sd’
FBNormalization: no visible global function definition for
  ‘write.table’
medianFilter: no visible global function definition for ‘median’
Undefined global functions or variables:
  bmp dev.print hist kmeans median par read.table sd write.table
Consider adding
  importFrom("grDevices", "bmp", "dev.print")
  importFrom("graphics", "hist", "par")
  importFrom("stats", "kmeans", "median", "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Rd file 'FBNormalization.Rd':
  \usage lines wider than 90 characters:
             normDataFileName = NULL, debugFlag = FALSE, plotFlag = FALSE, plotAndSaveFlag = FALSE)

These lines will be truncated in the PDF manual.
Packages required but not available: 'timeSeries', 'fBasics'

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.
Packages suggested but not available for checking: 'speedglm', 'glmnet'
‘library’ or ‘require’ calls in package code:
  ‘RCurl’ ‘RJSONIO’ ‘XML’ ‘glmnet’ ‘httr’ ‘speedglm’ ‘tcltk’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fbroc.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘BayesFactor’
Running examples in ‘fbst-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: access-method
> ### Title: Returns an object from an object of class 'fbst'.
> ### Aliases: $,fbst-method
> 
> ### ** Examples
> 
> set.seed(57)
> grp1=rnorm(50,0,1.5)
> grp2=rnorm(50,0.8,3.2)
> 
> p = as.vector(BayesFactor::ttestBF(x=grp1,y=grp2, 
+   posterior = TRUE, iterations = 3000, 
+   rscale = "medium")[,4])
Error in loadNamespace(x) : there is no package called ‘BayesFactor’
Calls: as.vector ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘fbet.Rmd’ using rmarkdown
Quitting from lines 94-98 (fbet.Rmd) 
Error: processing vignette ‘fbet.Rmd’ failed with diagnostics:
there is no package called 'BayesFactor'
--- failed re-building ‘fbet.Rmd’

--- re-building ‘fbst.Rmd’ using rmarkdown
Quitting from lines 69-73 (fbst.Rmd) 
Error: processing vignette ‘fbst.Rmd’ failed with diagnostics:
there is no package called 'BayesFactor'
--- failed re-building ‘fbst.Rmd’

SUMMARY: processing the following files failed:
  ‘fbet.Rmd’ ‘fbst.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'arules', 'hasseDiagram'
Error(s) in re-building vignettes:
  ...
--- re-building ‘arules.Rmd’ using rmarkdown
Quitting from lines 25-27 (arules.Rmd) 
Error: processing vignette ‘arules.Rmd’ failed with diagnostics:
there is no package called 'arules'
--- failed re-building ‘arules.Rmd’

--- re-building ‘concept_lattice.Rmd’ using rmarkdown
Warning: You have not installed the 'hasseDiagram' package, which is needed to plot the lattice.
Warning: You have not installed the 'hasseDiagram' package, which is needed to plot the lattice.
Warning: You have not installed the 'hasseDiagram' package, which is needed to plot the lattice.
--- finished re-building ‘concept_lattice.Rmd’

--- re-building ‘conceptual-scaling.Rmd’ using rmarkdown
--- finished re-building ‘conceptual-scaling.Rmd’

--- re-building ‘extending_equivalence.Rmd’ using rmarkdown
--- finished re-building ‘extending_equivalence.Rmd’

--- re-building ‘implications.Rmd’ using rmarkdown
--- finished re-building ‘implications.Rmd’

SUMMARY: processing the following file failed:
  ‘arules.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.
Packages required but not available:
  'fields', 'spatstat.geom', 'bigsplines', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘kerdiest’

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 required but not available: ‘rstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'timeSeries', 'fBasics', 'fMultivar'

Package suggested but not available for checking: ‘sn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘semTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'MCL', 'ADPclust', 'flexclust', 'EMCluster', 'pdfCluster', 'plotly',
  'ProjectionBasedClustering', 'densityClust', 'R.utils', 'Spectrum',
  'genie', 'PPCI', 'clustrd', 'smacof', 'dendextend', 'prabclus',
  'mixtools', 'HDclassif', 'clustvarsel', 'clusterSim'
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test2delete.txt’ ‘test2delete2_values.txt’ ‘test2delete_values.txt’
Package required but not available: ‘fields’

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.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.Rprofile’
Packages required but not available: 'fda', 'vars'

Package suggested but not available for checking: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fdapace’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'fda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fda', 'doParallel', 'doBy', 'magic'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking: 'ks', 'EMCluster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fdapace', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geometry', 'plot3Drgl'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fdapace’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fds’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fields', 'doParallel'

Package suggested but not available for checking: ‘plot3Drgl’

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: 'fda', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fds’
'LazyData' is specified without a 'data' directory
Running examples in ‘fdcov-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: classifier-com
> ### Title: Functional data classifier via concentration inequalities
> ### Aliases: classifier-com classif.com predict.classif.com
> 
> ### ** Examples
> 
> ## Not run: 
> ##D  library(fds);
> ##D  # Setup training data
> ##D  dat1 = rbind( 
> ##D    t(aa$y[,1:100]), t(ao$y[,1:100]), t(dcl$y[,1:100]), 
> ##D    t(iy$y[,1:100]), t(sh$y[,1:100]) 
> ##D  );
> ##D  # Setup testing data
> ##D  dat2 = rbind( 
> ##D    t(aa$y[,101:400]), t(ao$y[,101:400]), t(dcl$y[,101:400]), 
> ##D    t(iy$y[,101:400]), t(sh$y[,101:400]) 
> ##D  );
> ##D  
> ##D  datgrp = gl(5,100);
> ##D  clCom = classif.com( datgrp, dat1 );
> ##D  grp = predict( clCom, dat2, LOADING=TRUE );
> ##D  acc = c(
> ##D    sum( grp[1:300]==1 ), sum( grp[301:600]==2 ), sum( grp[601:900]==3 ), 
> ##D    sum( grp[901:1200]==4 ), sum( grp[1201:1500]==5 )
> ##D  )/300;
> ##D  print(rbind(gl(5,1),signif(acc,3)));
> ## End(Not run)
> ## Don't show: 
>  library(fds);
Error in library(fds) : there is no package called ‘fds’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Quitting from lines 29-41 (vignette.Rmd) 
Error: processing vignette ‘vignette.Rmd’ failed with diagnostics:
there is no package called 'rainbow'
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'rtdists', 'ggforce'
Error(s) in re-building vignettes:
  ...
--- re-building ‘benchmark.Rmd’ using rmarkdown
--- finished re-building ‘benchmark.Rmd’

--- re-building ‘example.Rmd’ using rmarkdown
--- finished re-building ‘example.Rmd’

--- re-building ‘math.Rmd’ using rmarkdown
--- finished re-building ‘math.Rmd’

--- re-building ‘pfddm.Rmd’ using rmarkdown
--- finished re-building ‘pfddm.Rmd’

--- re-building ‘validity.Rmd’ using rmarkdown
Quitting from lines 573-575 (validity.Rmd) 
Error: processing vignette ‘validity.Rmd’ failed with diagnostics:
there is no package called 'rtdists'
--- failed re-building ‘validity.Rmd’

SUMMARY: processing the following file failed:
  ‘validity.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'arules', 'car', 'caret', 'FactoMineR', 'flexclust', 'fpc', 'glmnet',
  'ibr', 'irr', 'mda', 'questionr', 'text2vec', 'wordcloud'

Package suggested but not available for checking: ‘fds’

Package which this enhances but not available for checking: ‘NMF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'doParallel', 'forecast', 'itertools', 'tseries', '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.
Packages required but not available: 'Fgmutils', 'sqldf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geometry', 'vegan'

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: 'fda', 'mosaic'

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.
Package required but not available: ‘rainbow’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FDX.Rcheck/00install.out’ for details.
Package required but not available: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rpart.plot', 'GA'

Package suggested but not available for checking: ‘doParallel’

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 suggested but not available for checking: ‘fable’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/feasts.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘rpart.plot’

Package suggested but not available for checking: ‘mlr’

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: ‘glmnet’
Error(s) in re-building vignettes:
  ...
--- re-building ‘FeatureHashing.Rmd’ using rmarkdown
Quitting from lines 68-98 (FeatureHashing.Rmd) 
Error: processing vignette ‘FeatureHashing.Rmd’ failed with diagnostics:
there is no package called 'glmnet'
--- failed re-building ‘FeatureHashing.Rmd’

--- re-building ‘SentimentAnalysis.Rmd’ using rmarkdown
--- finished re-building ‘SentimentAnalysis.Rmd’

SUMMARY: processing the following file failed:
  ‘FeatureHashing.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'flexclust', 'ClustImpute'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FeatureImpCluster.Rcheck/00install.out’ for details.
Package required but not available: ‘ks’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/features.Rcheck/00install.out’ for details.
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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'readr', 'vroom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'devtools', 'rgdal', 'raster', 'Hmisc', 'rgeos', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'mapdata', 'gstat', 'automap'

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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lme4', 'sae', 'fields', 'snowfall'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rstan', 'ergm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'gganimate', 'ggrepel', 'ggforce'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'timeSeries', 'fBasics', 'fGarch'

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/FFD.Rcheck/00install.out’ for details.
‘library’ or ‘require’ calls in package code:
  ‘ggplot2’ ‘gridExtra’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
FFieldPtRepDemo: no visible global function definition for ‘ggplot’
FFieldPtRepDemo: no visible binding for global variable ‘mtcars’
FFieldPtRepDemo: no visible global function definition for ‘aes’
FFieldPtRepDemo: no visible binding for global variable ‘mpg’
FFieldPtRepDemo: no visible global function definition for ‘geom_point’
FFieldPtRepDemo: no visible global function definition for ‘geom_text’
FFieldPtRepDemo: no visible global function definition for ‘ggtitle’
FFieldPtRepDemo: no visible global function definition for
  ‘geom_segment’
FFieldPtRepDemo: no visible global function definition for
  ‘grid.arrange’
Undefined global functions or variables:
  aes geom_point geom_segment geom_text ggplot ggtitle grid.arrange mpg
  mtcars
Consider adding
  importFrom("datasets", "mtcars")
to your NAMESPACE file.
Package suggested but not available for checking: ‘car’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘NlcOptim’

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: ‘biglm’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ff.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:
  > suppressPackageStartupMessages({
  +   library(testthat)
  +   library(httptest)
  +   library(checkmate)
  +   library(ffscrapr)
  + })
  Error in library(httptest) : there is no package called 'httptest'
  Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
  Execution halted
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/ffstream.Rcheck/00install.out’ for details.
ftest: no visible global function definition for ‘wilcox.test’
ftest: no visible global function definition for ‘t.test’
Undefined global functions or variables:
  t.test wilcox.test
Consider adding
  importFrom("stats", "t.test", "wilcox.test")
to your NAMESPACE file.
Packages required but not available: 'timeSeries', 'fBasics'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'jpmesh', 'raster', 'readr', 'stars'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fgeo.tool’

Packages suggested but not available for checking: 'fgeo.plot', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fgeo.tool', 'ggrepel'

Package suggested but not available for checking: ‘fgeo.analyze’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fgeo.analyze', 'fgeo.plot', 'fgeo.tool'

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: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sna', 'lmtest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'JGL', 'fdapace'

Package suggested but not available for checking: ‘fda’

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.
fgeasy: no visible global function definition for ‘dist’
fgeasy : cor.est: no visible global function definition for ‘cor.test’
fgeasy: no visible binding for global variable ‘var’
fgperm : runrand: no visible global function definition for ‘runif’
fgperm : runrand: no visible global function definition for ‘ave’
fgploc : runrand: no visible global function definition for ‘runif’
fgploc : runrand: no visible global function definition for ‘ave’
fyshuffle: no visible global function definition for ‘runif’
plot.fg: no visible global function definition for ‘par’
plot.fg: no visible global function definition for ‘segments’
plot.fg: no visible binding for global variable ‘quantile’
plot.fg: no visible global function definition for ‘abline’
plot.fg: no visible global function definition for ‘axis’
summary.fg: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  abline ave axis cor.test dist par quantile runif segments var
Consider adding
  importFrom("graphics", "abline", "axis", "par", "segments")
  importFrom("stats", "ave", "cor.test", "dist", "quantile", "runif",
             "var")
to your NAMESPACE file.
Packages suggested but not available for checking: 'doSNOW', 'tseries'
Error(s) in re-building vignettes:
  ...
--- re-building ‘fHMM.Rmd’ using rmarkdown
--- finished re-building ‘fHMM.Rmd’

--- re-building ‘v01_model_definition.Rmd’ using rmarkdown
--- finished re-building ‘v01_model_definition.Rmd’

--- re-building ‘v02_controls.Rmd’ using rmarkdown
--- finished re-building ‘v02_controls.Rmd’

--- re-building ‘v03_data_management.Rmd’ using rmarkdown
--- finished re-building ‘v03_data_management.Rmd’

--- re-building ‘v04_model_estimation.Rmd’ using rmarkdown
--- finished re-building ‘v04_model_estimation.Rmd’

--- re-building ‘v05_state_decoding_and_prediction.Rmd’ using rmarkdown
--- finished re-building ‘v05_state_decoding_and_prediction.Rmd’

--- re-building ‘v06_model_checking.Rmd’ using rmarkdown
Quitting from lines 62-64 (v06_model_checking.Rmd) 
Error: processing vignette ‘v06_model_checking.Rmd’ failed with diagnostics:
there is no package called 'tseries'
--- failed re-building ‘v06_model_checking.Rmd’

--- re-building ‘v07_model_selection.Rmd’ using rmarkdown
--- finished re-building ‘v07_model_selection.Rmd’

SUMMARY: processing the following file failed:
  ‘v06_model_checking.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘interval’

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:
  'msm', 'flexsurv', 'sn', 'GGally'
Error(s) in re-building vignettes:
  ...
--- re-building ‘fic.Rnw’ using knitr
--- finished re-building ‘fic.Rnw’

--- re-building ‘linear.Rnw’ using knitr
--- finished re-building ‘linear.Rnw’

--- re-building ‘loss.Rnw’ using knitr
--- finished re-building ‘loss.Rnw’

--- re-building ‘multistate.Rnw’ using knitr
Quitting from lines 114-125 (multistate.Rnw) 
Error: processing vignette ‘multistate.Rnw’ failed with diagnostics:
The `msm` package should be installed
to run code in this vignette
--- failed re-building ‘multistate.Rnw’

--- re-building ‘skewnormal.Rnw’ using knitr
Quitting from lines 71-78 (skewnormal.Rnw) 
Error: processing vignette ‘skewnormal.Rnw’ failed with diagnostics:
The `sn` package should be installed to run code in this vignette
--- failed re-building ‘skewnormal.Rnw’

--- re-building ‘survival.Rnw’ using knitr
Quitting from lines 46-52 (survival.Rnw) 
Error: processing vignette ‘survival.Rnw’ failed with diagnostics:
The `flexsurv` package should be installed
to run code in this vignette
--- failed re-building ‘survival.Rnw’

SUMMARY: processing the following files failed:
  ‘multistate.Rnw’ ‘skewnormal.Rnw’ ‘survival.Rnw’

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: ‘phyloseq’

Packages suggested but not available for checking: 'MCMCpack', 'MicrobeDS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'caret', 'vegan', 'rgeos'

Packages suggested but not available for checking:
  'imager', 'rgdal', 'RStoolbox', 'maptools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FieldSim.Rcheck/00install.out’ for details.
Package required but not available: ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'JoSAE', 'mase', 'rgdal', 'RPostgreSQL', 'RSQLite', 'sae', 'sqldf'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘microeco’

Packages suggested but not available for checking:
  'Biostrings', 'seqinr', 'phyloseq'

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.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RSQLite’
Package suggested but not available for checking: ‘io’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘strex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘CVXR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘timeSeries’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GGally', 'lme4'

Packages suggested but not available for checking:
  'cmprsk', 'coxme', 'lmtest', 'readr', 'rstan', 'survey', 'survminer'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'quantmod', 'xts', 'TTR'

Package suggested but not available for checking: ‘timeSeries’

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: ‘readODS’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘R.utils’
Packages required but not available: 'arm', 'glmnet', 'lmtest'

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: ‘diveRsity’
Found the following files/directories:
  ‘AH_genepop.txt’ ‘AH_popname.txt’ ‘JSM_MS_freq.txt’
  ‘JSM_MS_genepop.txt’ ‘JSM_genepop_clipped_both.txt’
  ‘JSM_genepop_clipped_maf.txt’ ‘JSM_genepop_clipped_name.txt’
  ‘JSM_mtDNA_freq.txt’ ‘JSM_popname.txt’ ‘result_DJ.csv’
  ‘result_EBDJ.csv’ ‘result_EBFST.csv’ ‘result_EBFST_mtDNA.csv’
  ‘result_EBGstH.csv’ ‘result_GstH.csv’ ‘result_GstN.csv’
  ‘result_GstNC.csv’ ‘result_thetaWCpair.csv’
Packages required but not available: 'tune', 'dials'

Packages suggested but not available for checking:
  'BradleyTerry2', 'discrim', 'klaR', 'lme4', 'recipes', 'rsample'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'klaR', 'GGally', 'Rcmdr', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'modeltime', 'Cubist', 'dials', 'doParallel', 'earth', 'glmnet',
  'hts', 'modeltime.gluonts', 'modeltime.resample', 'recipes',
  'rsample', 'rules', 'timetk', 'tune'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'distrEx', 'tseries', 'lmtest'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FinTS.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package required but not available: ‘jose’

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: ‘DiagrammeR’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Data-Model.Rmd’ using rmarkdown

Attaching package: 'dm'

The following object is masked from 'package:stats':

    filter

Quitting from lines 18-27 (Data-Model.Rmd) 
Error: processing vignette ‘Data-Model.Rmd’ failed with diagnostics:
there is no package called 'DiagrammeR'
--- failed re-building ‘Data-Model.Rmd’

--- re-building ‘fishdata-examples.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

`summarise()` has grouped output by 'site'. You can override using the
`.groups` argument.
--- finished re-building ‘fishdata-examples.Rmd’

SUMMARY: processing the following file failed:
  ‘Data-Model.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘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/FisHiCal.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/fishmove.Rcheck/00install.out’ for details.
Packages required but not available: 'geiger', 'phytools', 'rfishbase'

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.
Packages required but not available: 'rMR', 'respirometry'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'diversitree', 'geiger', 'hisse', 'phytools', 'picante', 'rfishbase'
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘community-analysis.Rmd’ using rmarkdown
--- finished re-building ‘community-analysis.Rmd’

--- re-building ‘comparative-analysis.Rmd’ using rmarkdown
Quitting from lines 41-48 (comparative-analysis.Rmd) 
Error: processing vignette ‘comparative-analysis.Rmd’ failed with diagnostics:
there is no package called 'rfishbase'
--- failed re-building ‘comparative-analysis.Rmd’

SUMMARY: processing the following file failed:
  ‘comparative-analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘rfishbase’
Package required but not available: ‘bestglm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'viridis', 'varian', 'leaflet', 'leafgl', 'raster', 'rayshader'

Packages suggested but not available for checking: 'CopernicusDEM', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'mc2d', 'gamlss.dist', 'Hmisc'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fitdistrplus.Rcheck/00install.out’ for details.
Packages required but not available: 'ICSNP', 'ghyp'

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: ‘devtools’
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘doParallel’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'maxLik', 'R.utils'

Packages suggested but not available for checking:
  'DiscreteInverseWeibull', 'DiscreteWeibull', 'emg', 'FatTailsR',
  'fBasics', 'fExtremes', 'flexsurv', 'gambin', 'gb', 'GLDEX',
  'glogis', 'GSM', 'hermite', 'KScorrect', 'marg', 'mc2d', 'msm',
  'ParetoPosStable', 'qmap', 'QRM', 'ReIns', 'reliaR', 'Renext',
  'sadists', 'sn', 'STAR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'doMC', 'RSvgDevice'
‘library’ or ‘require’ calls in package code:
  ‘devEMF’ ‘doMC’ ‘foreach’ ‘grDevices’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following files/directories:
  ‘modelfile.dat’ ‘plots’ ‘scorefile.dat’
Package required but not available: ‘fitdistrplus’

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: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'readr', 'fivethirtyeightdata'
Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
Error(s) in re-building vignettes:
  ...
--- re-building ‘fivethirtyeight.Rmd’ using rmarkdown
Some larger datasets need to be installed separately, like senators and
house_district_forecast. To install these, we recommend you install the
fivethirtyeightdata package by running:
install.packages('fivethirtyeightdata', repos =
'https://fivethirtyeightdata.github.io/drat/', type = 'source')

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 13-63 (fivethirtyeight.Rmd) 
Error: processing vignette ‘fivethirtyeight.Rmd’ failed with diagnostics:
there is no package called 'readr'
--- failed re-building ‘fivethirtyeight.Rmd’

--- re-building ‘tame.Rmd’ using rmarkdown
--- finished re-building ‘tame.Rmd’

--- re-building ‘user_contributed_vignettes.Rmd’ using rmarkdown
--- finished re-building ‘user_contributed_vignettes.Rmd’

SUMMARY: processing the following file failed:
  ‘fivethirtyeight.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘doParallel’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FixedPoint.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'plm', 'lfe'
Packages suggested but not available for checking: 'multxpert', 'multcomp'
'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/FKSUM.Rcheck/00install.out’ for details.
Package required but not available: ‘mlr’

Packages suggested but not available for checking:
  'devtools', 'mda', 'plotly', 'R.rsp', 'smoof'

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: ‘eurostat’
'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: ‘ggforce’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/flare.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Package required but not available: ‘rpart.plot’

Packages suggested but not available for checking:
  'caret', 'mlr3', 'mlr3learners'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/flatr.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘seriation’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/flexclust.Rcheck/00install.out’ for details.
Package required but not available: ‘ContaminatedMixt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'FactoMineR', 'sisal', 'dendextend', 'ggforce'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘scam’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'MonoPoly', 'mirt'
Error(s) in re-building vignettes:
  ...
--- re-building ‘fmp.Rmd’ using rmarkdown
Quitting from lines 118-123 (fmp.Rmd) 
Error: processing vignette ‘fmp.Rmd’ failed with diagnostics:
there is no package called 'MonoPoly'
--- failed re-building ‘fmp.Rmd’

SUMMARY: processing the following file failed:
  ‘fmp.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘flexmix’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'Ecdat', 'gclus', 'glmnet', 'lme4', 'multcomp'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/flexmix.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FlexParamCurve.Rcheck/00install.out’ for details.
Packages required but not available: 'rstan', 'faraway'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Epi’

Package suggested but not available for checking: ‘relsurv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'smerc', 'spdep', 'spatialreg'

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.
Packages required but not available: 'mstate', 'rstpm2'

Packages suggested but not available for checking: 'msm', 'TH.data'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘equatags’
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘introduction.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.
Packages required but not available:
  'ggsn', 'ggmap', 'CircStats', 'fields', 'maptools', 'rgdal', 'rgeos'

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', 'tidyverse'

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’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/flippant.Rcheck/00install.out’ for details.
Package required but not available: ‘dials’

Packages suggested but not available for checking: 'tidyverse', 'plotly'

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: ‘TLMoments’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
RIind: no visible global function definition for ‘aggregate’
RIind: no visible binding for global variable ‘sd’
RIpop: no visible global function definition for ‘aggregate’
RIpop: no visible binding for global variable ‘sd’
SI: no visible global function definition for ‘sd’
SI2: no visible global function definition for ‘sd’
SI3: no visible global function definition for ‘aggregate’
SI3: no visible global function definition for ‘pairs’
SI3: no visible global function definition for ‘cor’
SI4: no visible global function definition for ‘aggregate’
SI4: no visible global function definition for ‘sd’
fCV: no visible global function definition for ‘sd’
Undefined global functions or variables:
  aggregate cor pairs sd
Consider adding
  importFrom("graphics", "pairs")
  importFrom("stats", "aggregate", "cor", "sd")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
‘library’ or ‘require’ call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
GCV: no visible global function definition for ‘lm’
GCV: no visible global function definition for ‘resid’
ffplot: no visible global function definition for ‘par’
ffplot: no visible global function definition for ‘points’
ffplot: no visible global function definition for ‘legend’
flowfield: no visible global function definition for ‘write.table’
gpr: no visible global function definition for ‘quantile’
gpr: no visible global function definition for ‘var’
smoothp: no visible global function definition for ‘lm’
smoothp: no visible global function definition for ‘predict’
smoothp: no visible global function definition for ‘resid’
smoothp: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  legend lm optimize par points predict quantile resid var write.table
Consider adding
  importFrom("graphics", "legend", "par", "points")
  importFrom("stats", "lm", "optimize", "predict", "quantile", "resid",
             "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Package required but not available: ‘styler’

Package suggested but not available for checking: ‘esquisse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'params', 'diagram', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'zyp', 'changepoint'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FLR.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FluMoDL.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/flux.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’
Packages required but not available: 'fitdistrplus', 'STAR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘forecast’

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
Package required but not available: ‘orthopolynom’

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: ‘diagram’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FME.Rcheck/00install.out’ for details.
Packages required but not available: 'flexmix', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'caret', 'solitude', 'C50', 'FactoMineR', 'factoextra'

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: 'Biobase', 'expm'

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: 'metafor', 'aws'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ciftiTools', 'ggpubr', 'neurobase'
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 ‘tp’ with type ‘arma::vec’ {aka ‘arma::Col<double>’} [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fMRIscrub.Rcheck/00install.out’ for details.
Unavailable namespace imported from by a ‘:::’ call: ‘ciftiTools’
  See the note in ?`:::` about the use of this operator.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Build --> Install and Restart
  > # [Edit this] path to the Workbench for your computer.
  > my_wb <- "../workbench"
  > 
  > library(testthat)
  > library(ciftiTools)
  Error in library(ciftiTools) : there is no package called 'ciftiTools'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘projection_scrubbing.rmd’ using rmarkdown
Quitting from lines 84-86 (projection_scrubbing.rmd) 
Error: processing vignette ‘projection_scrubbing.rmd’ failed with diagnostics:
there is no package called 'neurobase'
--- failed re-building ‘projection_scrubbing.rmd’

SUMMARY: processing the following file failed:
  ‘projection_scrubbing.rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'Epi', 'vcd'
BSOptionValue: no visible global function definition for ‘pnorm’
ImpliedVol: no visible global function definition for ‘uniroot’
callFMstable: no visible global function definition for ‘integrate’
fitGivenQuantile: no visible global function definition for ‘uniroot’
matchQuartiles: no visible global function definition for ‘optim’
putFMstable: no visible global function definition for ‘integrate’
standardStableQuantile: no visible global function definition for
  ‘qnorm’
tailsGstable: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate optim pnorm qnorm uniroot
Consider adding
  importFrom("stats", "integrate", "optim", "pnorm", "qnorm", "uniroot")
to your NAMESPACE file.
Packages required but not available: 'timeSeries', 'fBasics', 'sn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘chemometrics’
checkRd: (7) KL.dist.Rd:35: invalid email address: lishengqiao@yahoo.com.
checkRd: (7) KL.divergence.Rd:36: invalid email address: lishengqiao@yahoo.com.
checkRd: (7) crossentropy.Rd:27: invalid email address: lishengqiao@yahoo.com.
checkRd: (7) entropy.Rd:19: invalid email address: lishengqiao@yahoo.com.
checkRd: (7) get.knn.Rd:43: invalid email address: lishengqiao@yahoo.com.
checkRd: (7) knn.Rd:30: invalid email address: lishengqiao@yahoo.com.
checkRd: (7) knn.cv.Rd:33: invalid email address: lishengqiao@yahoo.com.
checkRd: (7) knn.dist.Rd:28: invalid email address: lishengqiao@yahoo.com.
checkRd: (7) knn.index.Rd:28: invalid email address: lishengqiao@yahoo.com.
checkRd: (7) knn.reg.Rd:49: invalid email address: lishengqiao@yahoo.com.
checkRd: (7) mutual_information.Rd:28: invalid email address: lishengqiao@yahoo.com.
checkRd: (7) ownn.rd:27: invalid email address: lishengqiao@yahoo.com.
checkRd: (7) print.knnRegCV.Rd:19: invalid email address: lishengqiao@yahoo.com.
Packages required but not available: 'timeSeries', 'fBasics'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FOCI.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'trip', 'furrr', 'CircStats', 'tmvtnorm'

Packages suggested but not available for checking: 'rgeos', 'rworldmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'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: 'viridis', 'ggraph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/foodweb.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rstan', 'arm', 'tidyverse'

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
Error(s) in re-building vignettes:
  ...
--- re-building ‘footprint.Rmd’ using rmarkdown
Quitting from lines 21-25 (footprint.Rmd) 
Error: processing vignette ‘footprint.Rmd’ failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘footprint.Rmd’

SUMMARY: processing the following file failed:
  ‘footprint.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘vegan’

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: 'doMC', 'doParallel'
Running ‘testthat.R’ [8s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(foreach)
  > 
  > 
  > Sys.setenv(FOREACH_BACKEND="SEQ")
  > test_check("foreach")
   Sequential backend[ FAIL 0 | WARN 0 | SKIP 0 | PASS 570 ]
  > 
  > Sys.setenv(FOREACH_BACKEND="PAR")
  > test_check("foreach")
  Error in loadNamespace(x) : there is no package called 'doParallel'
  Calls: test_check ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Package suggested but not available for checking: ‘fBasics’
Package required but not available: ‘quantreg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'forecast', 'mtsdi', 'quantreg'

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: 'forecast', 'thief', 'doParallel'

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: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lmtest', 'tseries'

Package suggested but not available for checking: ‘forecTheta’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'PSF', 'decomposedPSF', 'imputeTestbench', '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/FoReco.Rcheck/00install.out’ for details.
Packages required but not available: 'forecast', 'tseries'

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/forensim.Rcheck/00install.out’ for details.
Packages required but not available: 'GA', 'doParallel', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘blockCV’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'raster', 'viridis', 'rgeos', 'spatstat.core', 'spatstat.geom'

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: 'systemfit', 'ggpmisc', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'metafor', 'labelled'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/forestmodel.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/forestplot.Rcheck/00install.out’ for details.
Package required but not available: ‘partykit’

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: ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'APfun', 'doParallel', 'imager', 'raster', '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: ‘raster’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ForImp.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
INFCvpe: no visible binding for global variable ‘INFCstats’
INFCvpe: no visible binding for global variable ‘INFCdomain’
Undefined global functions or variables:
  INFCdomain INFCstats
'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: ‘meta’
Error(s) in re-building vignettes:
  ...
--- re-building ‘forplo_vignette.Rmd’ using rmarkdown
Quitting from lines 492-540 (forplo_vignette.Rmd) 
Error: processing vignette ‘forplo_vignette.Rmd’ failed with diagnostics:
there is no package called 'meta'
--- failed re-building ‘forplo_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘forplo_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'pedtools', 'pedprobr', 'ribd'

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/forward.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ForwardSearch.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'FactoMineR', 'likert'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Overview.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 25-33 (Overview.Rmd) 
Error: processing vignette ‘Overview.Rmd’ failed with diagnostics:
there is no package called 'FactoMineR'
--- failed re-building ‘Overview.Rmd’

SUMMARY: processing the following file failed:
  ‘Overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘shapefiles’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘TreeSim’

Packages suggested but not available for checking: 'paleotree', 'devtools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'raster', 'RStoolbox', 'spatstat.geom', 'spatstat', 'rgdal', 'caret'

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.
'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: ‘doSNOW’

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/FPCA2D.Rcheck/00install.out’ for details.
Packages required but not available: 'flexmix', 'prabclus'

Package suggested but not available for checking: ‘pdfCluster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ExPosition', 'klaR', 'GGally'

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fplot.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fplyr.Rcheck/00install.out’ for details.
Packages required but not available:
  'timeSeries', 'fBasics', 'fAssets', 'fCopulae', 'Rglpk', 'rneos'

Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2', 'dplR', 'fGarch', 'mvoutlier'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'expsmooth', 'fma', 'forecast'

Packages suggested but not available for checking:
  'GGally', 'Mcomp', 'tidyverse', 'vars'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fable', 'feasts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'forecast', 'fma', 'expsmooth', 'lmtest', 'tseries'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘forecast’
Package required but not available: ‘clusterGeneration’

Packages suggested but not available for checking: 'gstat', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘emg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'RandomFields', 'snowFT'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fractaldim.Rcheck/00install.out’ for details.
Package required but not available: ‘imager’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'metafor', 'netmeta'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘msm’

Packages suggested but not available for checking: 'plotly', 'egg'

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 required but not available: 'survC1', '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/frailtySurv.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/frair.Rcheck/00install.out’ for details.
Packages required but not available: 'bit64', 'rio', 'readr', 'vroom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Rglpk', 'timeSeries'

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 ‘lala2015pmml.Rtex’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘lala2015pmml.Rtex’ using ‘UTF-8’... failed to complete the test
Package required but not available: ‘calibrate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fdadensity', 'fdapace'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘xts’
Package required but not available: ‘disordR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘magic’

Package suggested but not available for checking: ‘permutations’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'smacof', 'vegan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'gifti', 'cifti'
Running examples in ‘freesurferformats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: write.fs.label.gii
> ### Title: Write a binary surface label in GIFTI format.
> ### Aliases: write.fs.label.gii
> 
> ### ** Examples
> 
>   label = c(1L, 23L, 44L); # the positive vertex indices
>   outfile = tempfile(fileext=".gii");
>   write.fs.label.gii(outfile, label, 50L);
Error in gifti_xml(list(label), intent = "NIFTI_INTENT_LABEL", datatype = "NIFTI_TYPE_INT32") : 
  Writing files in GIFTI format requires the 'gifti' package to be installed.
Calls: write.fs.label.gii -> gifti_xml
Execution halted
Packages required but not available: 'glmertree', 'pre', 'WGCNA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'timeSeries', 'fBasics', 'lmtest'

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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'fda', 'freqdom'

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/freqdom.Rcheck/00install.out’ for details.
Package required but not available: ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/freqpcr.Rcheck/00install.out’ for details.
Package required but not available: ‘vars’

Packages suggested but not available for checking: 'mAr', 'BigVAR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘haven’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/frequency.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/frequentistSSD.Rcheck/00install.out’ for details.
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking:
  'cvTools', 'glmnet', 'mRMRe', 'epiR', 'DescTools', 'irr',
  'survminer', 'BeSS', 'mda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘FrF2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DoE.base’

Package suggested but not available for checking: ‘FrF2.catlg128’

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’
Packages required but not available: 'Hmisc', 'spacetime', 'ggpubr'

Packages suggested but not available for checking:
  'dggrids', 'gstat', 'INLA', 'mapproj', 'rgeos', 'rgdal', 'spdep',
  'splancs', 'verification'

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 suggested but not available for checking: ‘PDQutils’
Packages required but not available: 'micEcon', 'lmtest', 'plm'

Package suggested but not available for checking: ‘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/frontiles.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘Introduction.Rmd’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'cna', 'Rfast'

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.
Packages required but not available: 'car', 'lmtest'

Packages suggested but not available for checking:
  'DescTools', 'fishmethods', 'marked'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fields', 'viridis'

Package suggested but not available for checking: ‘sphereplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'caret', 'gsubfn'

Packages suggested but not available for checking:
  'ada', 'arm', 'bst', 'C50', 'car', 'Cubist', 'earth', 'elasticnet',
  'evtree', 'extraTrees', 'foba', 'gam', 'glmnet', 'HDclassif',
  'Hmisc', 'ipred', 'klaR', 'LogicReg', 'mboost', 'mda', 'obliqueRF',
  'pamr', 'partDSA', 'party', 'penalized', 'quantregForest', 'relaxo',
  'rocc', 'rrcov', 'rrlda', 'RSNNS', 'sda', 'sparseLDA'

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: ‘rrcov’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'doParallel', 'RTCGA.rnaseq'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'caret', 'GA', 'prodlim'

Package suggested but not available for checking: ‘RSNNS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'readtext', 'R.utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'mpmi', 'freqdom', 'randomForestSRC'

Packages suggested but not available for checking: 'sparsevar', 'MTS'

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: ‘Rfast’

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.
GNU make is a SystemRequirements.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fSRM.Rcheck/00install.out’ for details.
Package required but not available: ‘glmnet’

Packages suggested but not available for checking: 'plotly', 'ggnetwork'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘SKAT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'bit64', 'nanotime'
Packages required but not available: 'timeSeries', 'fBasics'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'forecast', 'rainbow', 'sde', 'fda', 'pdfCluster', 'ecp',
  'strucchange', 'fGarch', 'vars', 'fdapace'

Packages suggested but not available for checking:
  'fds', 'R2jags', 'meboot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fts.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
Package required but not available: ‘snowfall’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'lme4', 'afex'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'devtools', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘biclust’

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 suggested but not available for checking:
  'DescTools', 'DiffXTables', 'GridOnClusters'
Error(s) in re-building vignettes:
  ...
--- re-building ‘adapted.fun.chisq.test.Rmd’ using rmarkdown
Loading required package: FunChisq
Loading required package: infotheo
Loading required package: DescTools
Quitting from lines 127-133 (adapted.fun.chisq.test.Rmd) 
Error: processing vignette ‘adapted.fun.chisq.test.Rmd’ failed with diagnostics:
could not find function "Untable"
--- failed re-building ‘adapted.fun.chisq.test.Rmd’

--- re-building ‘exact.fun.test.Rmd’ using rmarkdown
--- finished re-building ‘exact.fun.test.Rmd’

--- re-building ‘fun.chisq.test.Rmd’ using rmarkdown
--- finished re-building ‘fun.chisq.test.Rmd’

--- re-building ‘patterns.Rmd’ using rmarkdown
--- finished re-building ‘patterns.Rmd’

SUMMARY: processing the following file failed:
  ‘adapted.fun.chisq.test.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'fda.usc', 'fda', 'ggpubr', 'caret', 'flux', '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’
Errors in running code in vignettes:
when running code in ‘a.Overview.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?
when running code in ‘b.Simplest_use.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?
when running code in ‘c.Options_fclust.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?
when running code in ‘d.Options_fclust_plot.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?
when running code in ‘e.Multi_functionality.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?
when running code in ‘f.Test_clustering.Rmd’
  ...
Error in loadVignetteBuilder(pkgdir) : vignette builder ‘R.rsp’ not found
Calls: <Anonymous> -> loadVignetteBuilder
Execution halted

... incomplete output.  Crash?

  ‘a.Overview.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘b.Simplest_use.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘c.Options_fclust.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘d.Options_fclust_plot.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘e.Multi_functionality.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘f.Test_clustering.Rmd’ using ‘UTF-8’... failed to complete the test
Malformed Description field: should contain one or more complete sentences.
Package required but not available: ‘fields’

Package suggested but not available for checking: ‘fda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'future.apply', 'geometry', 'vegan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fda', 'elasticnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘CVXR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘doFuture’

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.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'timeSeries', 'fBasics'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fda', 'funFEM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'refund', 'tvem'

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: ‘ggrepel’

Package suggested but not available for checking: ‘COUNT’

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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Ecdat’
Package required but not available: ‘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/furrr.Rcheck/00install.out’ for details.
Packages required but not available: 'devtools', 'parsermd'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'irlba', '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/futile.paradigm.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘completeTrial_byArm_eventPriorRateC3=0.001_eventPriorRateT1=0_eventPriorRateT2=0_eventPriorWt=0.5.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.2.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.4.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.6.RData’
  ‘completeTrial_pooled_eventPriorRate=0.001_eventPriorWt=0.5.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.2.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.4.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.6.RData’
  ‘rcdf_byArm_arm=T1_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03.pdf’
  ‘rcdf_pooled_eventPriorRate=0.06.pdf’
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/future.apply.Rcheck/00install.out’ for details.
Skipping vignette re-building
Packages suggested but not available for checking: 'future.apply', '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/future.batchtools.Rcheck/00install.out’ for details.
Skipping vignette re-building
Packages suggested but not available for checking: 'future.apply', '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/future.callr.Rcheck/00install.out’ for details.
Package required but not available: ‘leaflet’

Package suggested but not available for checking: ‘mapproj’

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/FuzzyAHP.Rcheck/00install.out’ for details.
Package required but not available: ‘doParallel’

Package suggested but not available for checking: ‘WGCNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'readr', 'IRanges'
Package unavailable to check Rd xrefs: ‘IRanges’
Package required but not available: ‘ROI.plugin.glpk’

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 suggested but not available for checking: 'maptools', 'raster'
Skipping vignette re-building
Packages suggested but not available for checking: 'markovchain', '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/FuzzySTs.Rcheck/00install.out’ for details.
NeedsCompilation field must take value ‘yes’ or ‘no’
‘library’ or ‘require’ call to ‘splines’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gensurf: no visible global function definition for ‘persp’
gensurf: no visible global function definition for ‘rainbow’
plotMF: no visible global function definition for ‘plot.new’
plotMF: no visible global function definition for ‘plot.window’
plotMF: no visible global function definition for ‘runif’
plotMF: no visible global function definition for ‘predict’
plotMF: no visible global function definition for ‘interpSpline’
plotMF: no visible global function definition for ‘lines’
plotMF: no visible global function definition for ‘text’
plotMF: no visible global function definition for ‘title’
plotMF: no visible global function definition for ‘axis’
plotMF: no visible global function definition for ‘box’
Undefined global functions or variables:
  axis box interpSpline lines persp plot.new plot.window predict
  rainbow runif text title
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "persp", "plot.new",
             "plot.window", "text", "title")
  importFrom("stats", "predict", "runif")
to your NAMESPACE file.
Rd file 'newFIS.Rd':
  \usage lines wider than 90 characters:
     newFIS(FISName, FISType = "mamdani", version = "1.0", andMethod = "min", orMethod = "max", impMethod = "min", aggMethod = "max", defuzz ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Package required but not available: ‘cvTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Matrix.utils’

Packages suggested but not available for checking: 'lfe', 'ivreg', 'lmtest'

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: 'strucchange', 'car'

Package suggested but not available for checking: ‘lmtest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doFuture', 'JOPS'

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/G1DBN.Rcheck/00install.out’ for details.
Packages required but not available: 'KEGGREST', 'sybil'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xlsx', 'xlsxjars'

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.
Package suggested but not available for checking: ‘ArrayBin’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GABi.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GADAG.Rcheck/00install.out’ for details.
FPTsimul: no visible global function definition for ‘runif’
histplot: no visible global function definition for ‘dev.new’
histplot: no visible global function definition for ‘hist’
histplot: no visible global function definition for ‘par’
histplot: no visible global function definition for ‘legend’
mdt: no visible binding for global variable ‘deltat’
plot.FPTdensity: no visible global function definition for ‘dev.new’
res_summary: no visible global function definition for ‘write.table’
res_summary: no visible global function definition for ‘sd’
res_summary: no visible global function definition for ‘median’
vdt: no visible binding for global variable ‘deltat’
Undefined global functions or variables:
  deltat dev.new hist legend median par runif sd write.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "hist", "legend", "par")
  importFrom("stats", "deltat", "median", "runif", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘results_Wiener1.out’
Packages required but not available:
  'rgdal', 'maptools', 'raster', 'rosm', 'rgeos', 'ggmap', 'ggspatial'

Package suggested but not available for checking: ‘mapproj’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GAD.Rcheck/00install.out’ for details.
Packages required but not available: 'maptools', '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.
CI.RMSEA: no visible global function definition for ‘qchisq’
CI.RMSEA: no visible global function definition for ‘pchisq’
GAIPE.RMSEA: no visible global function definition for ‘par’
GAIPE.RMSEA: no visible global function definition for ‘abline’
GAIPE.RMSEA: no visible global function definition for ‘colors’
GAIPE.RMSEA: no visible global function definition for ‘text’
GAIPE.RMSEA: no visible global function definition for ‘arrows’
GAIPE.RMSEA: no visible global function definition for ‘points’
GAIPE.RMSEA: no visible global function definition for ‘axis’
GAIPE.RMSEA: no visible global function definition for ‘lines’
GAIPE.RMSEA: no visible global function definition for ‘legend’
GAIPE.RMSEA: no visible global function definition for ‘pchisq’
GAIPE.RMSEA: no visible global function definition for ‘qchisq’
GAIPE.RMSEA: no visible global function definition for ‘mtext’
GAIPE.RMSEA: no visible global function definition for ‘title’
PA.RMSEA: no visible global function definition for ‘pchisq’
PA.RMSEA: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  abline arrows axis colors legend lines mtext par pchisq points qchisq
  text title
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "abline", "arrows", "axis", "legend", "lines",
             "mtext", "par", "points", "text", "title")
  importFrom("stats", "pchisq", "qchisq")
to your NAMESPACE file.
Package suggested but not available for checking: ‘taxize’
Package required but not available: ‘ryandexdirect’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'rtracklayer'

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/galts.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'lme4', 'geoR'
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gganimate', 'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mboost’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘latticeExtra’

Packages suggested but not available for checking:
  'quantreg', 'diagram', 'forecast', 'Ecdat', 'DAAGbio', 'car', 'DAAG'

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: ‘gam’

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 ‘gameR.Rmd’ using rmarkdown
Quitting from lines 20-24 (gameR.Rmd) 
Error: processing vignette ‘gameR.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- failed re-building ‘gameR.Rmd’

SUMMARY: processing the following file failed:
  ‘gameR.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘maxLik’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GameTheoryAllocation.Rcheck/00install.out’ for details.
Package required but not available: ‘kappalab’

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/gamlr.Rcheck/00install.out’ for details.
Packages required but not available: 'gamlss.dist', 'gamlss'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gamlss.dist', 'gamlss'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gamlss.dist', 'gamlss'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gamlss.dist', 'gamlss'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gamlss.dist', 'gamlss.tr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gamlss.dist.Rcheck/00install.out’ for details.
Packages required but not available:
  'gamlss', 'doParallel', 'gamlss.dist', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'gamlss.dist', 'gamlss', 'gamlss.foreach'

Package suggested but not available for checking: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gamlss', 'gamlss.dist'

Packages suggested but not available for checking:
  'gamlss.cens', 'gamlss.tr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gamlss', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gamlss.dist', 'gamlss'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gamlss’

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: 'gamlss.dist', 'gamlss', 'gamlss.add'

Packages suggested but not available for checking: 'spdep', 'maptools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gamlss.dist', 'gamlss'

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/gammSlice.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gam.Rcheck/00install.out’ for details.
Packages required but not available: 'glmnet', 'robustHD', '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: ‘Ecdat’
Package required but not available: ‘mda’

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 suggested but not available for checking: ‘GANPA’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GANPA.Rcheck/00install.out’ for details.
Packages required but not available: 'raster', 'tmap', 'fasterize'

Packages suggested but not available for checking: 'rgdal', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'doParallel', 'doRNG', 'caret'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GAparsimony.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: 'fields', 'quantreg'

Packages which this enhances but not available for checking:
  'raster', 'doParallel', 'doMPI'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gapmap.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'BradleyTerry2', 'MCMCglmm', 'R2jags', 'calibrate', 'coxme',
  'forestplot', 'genetics', 'haplo.stats', 'kinship2', 'magic', 'meta',
  'metafor', 'mets', 'pedigree', 'pedigreemm', 'plotly', 'rms'
‘gs+qpdf’ made some significant size reductions:
     compacted ‘jss.pdf’ from 427Kb to 166Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files
Error(s) in re-building vignettes:
  ...
--- re-building ‘gap.Rnw’ using Sweave
gap version 1.2.3-1

Error: processing vignette ‘gap.Rnw’ failed with diagnostics:
 chunk 1 
Error in library(kinship2) : there is no package called ‘kinship2’

--- failed re-building ‘gap.Rnw’

--- re-building ‘jss.Rnw’ using Sweave
--- finished re-building ‘jss.Rnw’

SUMMARY: processing the following file failed:
  ‘gap.Rnw’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'doParallel', 'doRNG'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/garchx.Rcheck/00install.out’ for details.
Package required but not available: ‘vcfR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'forecast', 'GA'

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: ‘chemometrics’
Package required but not available: ‘AICcmodavg’

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: ‘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/gaston.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'fields', 'raster', 'sparr', 'SpatialPack', 'spatstat.geom'

Packages suggested but not available for checking: 'ncdfFlow', '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’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘metR’

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: 'SSBtools', 'RegSDC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'FD', 'GA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘GB2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survey’

Package suggested but not available for checking: ‘simFrame’

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: ‘SKAT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gbm2sas.Rcheck/00install.out’ for details.
Packages required but not available:
  'dismo', 'maptools', 'rgdal', 'rgeos', 'raster', 'shapefiles'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'pdp', 'viridis'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gbmt.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gbp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gb.Rcheck/00install.out’ for details.
Package in Depends field not imported from: ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ‘:::’ calls:
  ‘tools:::.Rd_get_argument_names’ ‘tools:::RdTags’ ‘tools:::fetchRdDB’
  See the note in ?`:::` about the use of this operator.
Package required but not available: ‘rjags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'doRNG', 'earth'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'classGraph', 'graph', 'Rgraphviz'
coeplot: no visible global function definition for ‘axis’
coeplot: no visible global function definition for ‘lines’
coeplot: no visible global function definition for ‘title’
coeplot: no visible global function definition for ‘legend’
corplot: no visible global function definition for ‘par’
corplot: no visible global function definition for ‘pairs’
corplot: no visible global function definition for ‘strwidth’
lm.estimate: no visible global function definition for ‘as.formula’
lm.estimate: no visible global function definition for ‘glm’
panel.cor: no visible global function definition for ‘par’
panel.cor: no visible global function definition for ‘cor’
panel.cor: no visible global function definition for ‘strwidth’
panel.cor: no visible global function definition for ‘text’
panel.smooth.r: no visible global function definition for ‘par’
panel.smooth.r: no visible global function definition for ‘points’
panel.smooth.r: no visible global function definition for ‘lines’
posplot: no visible global function definition for ‘par’
posplot: no visible global function definition for ‘barplot’
posplot: no visible global function definition for ‘points’
Undefined global functions or variables:
  as.formula axis barplot cor glm legend lines pairs par points
  strwidth text title
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "pairs",
             "par", "points", "strwidth", "text", "title")
  importFrom("stats", "as.formula", "cor", "glm")
to your NAMESPACE file.
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘vegan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
gcat.test: no visible global function definition for ‘pnorm’
generate_sub: no visible global function definition for ‘runif’
pfcn: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm runif
Consider adding
  importFrom("stats", "pnorm", "runif")
to your NAMESPACE file.
Package required but not available: ‘RSQLite’

Package suggested but not available for checking: ‘gputools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gcdnet.Rcheck/00install.out’ for details.
Package required but not available: ‘raster’

Package suggested but not available for checking: ‘paleofire’

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 required but not available: 'wordcloud', 'tm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'EQL', 'gcmr', 'latticeExtra', 'snowfall'
Unknown package ‘gcmr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gclus.Rcheck/00install.out’ for details.
Package required but not available: ‘rjags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'arm', 'wiqid'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘stars’
Packages suggested but not available for checking:
  'raster', 'rgdal', 'rasterVis'
Found the following calls to attach():
File ‘g.data/R/g.data.attach.R’:
  attach(NULL, pos, basename(dir))
See section ‘Good practice’ in ‘?attach’.
checkRd: (7) rename.vars.Rd:50: invalid email address: macq\@llnl.gov
Running examples in ‘gdata-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: is.what
> ### Title: Run Multiple is.* Tests on a Given Object
> ### Aliases: is.what
> ### Keywords: classes NA programming error utilities
> 
> ### ** Examples
> 
> is.what(pi)
[1] "is.atomic"  "is.double"  "is.finite"  "is.numeric" "is.vector" 
> is.what(NA, verbose=TRUE)
                    is
is.array             .
is.atomic            T
is.call              .
is.character         .
is.complex           .
is.data.frame        .
is.double            .
is.environment       .
is.expression        .
is.factor            .
is.finite            .
is.function          .
is.hashtab           .
is.infinite          .
is.integer           .
is.language          .
is.leaf              .
is.levelsMap         .
is.list              .
is.listLevelsMap     .
is.logical           T
is.matrix            .
is.mts               .
is.na                T
is.na.POSIXlt        T
is.na.data.frame     T
is.name              .
is.nan               .
is.null              .
is.numeric           .
is.numeric.Date      .
is.numeric.POSIXt    .
is.numeric.difftime  .
is.numeric_version   .
is.object            .
is.object_sizes      .
is.ordered           .
is.package_version   .
is.pairlist          .
is.primitive         .
is.qr                .
is.raster            .
is.raw               .
is.recursive         .
is.relistable        .
is.stepfun           .
is.symbol            .
is.table             .
is.ts                .
is.tskernel          .
is.unsorted          .
is.vector            T
> is.what(lm(1~1))
Error in !is.logical(result) || is.na(result) : 
  'length = 11' in coercion to 'logical(1)'
Calls: is.what
Execution halted
Packages required but not available: 'FactoMineR', 'ggrepel', 'GGally'

Packages suggested but not available for checking:
  'WeightedCluster', 'vcd', '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: 'maptools', 'rgeos', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'leaflet', 'RSQLite', 'R.utils', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘grImport’
Package required but not available: ‘alabama’

Packages suggested but not available for checking: 'CDM', 'poLCA'

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', 'vegan', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xts', '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.
Package suggested but not available for checking: ‘magclass’
Running ‘testthat.R’ [56s/84s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(GDPuc)
  > 
  > test_check("GDPuc")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 311 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-check_user_input.R:16:3): gdp argument ──────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'magclass'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-check_user_input.R:16:2
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base withOneRestart(expr, restarts[[1L]])
   4.       └─base doWithOneRestart(return(expr), restart)
  ── Error (test-convertGDP.R:63:3): convertGDP magpie object ────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'magclass'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-convertGDP.R:63:2
   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 311 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘handle_NAs.Rmd’ using rmarkdown
--- finished re-building ‘handle_NAs.Rmd’

--- re-building ‘magpie.Rmd’ using rmarkdown
Quitting from lines 20-36 (magpie.Rmd) 
Error: processing vignette ‘magpie.Rmd’ failed with diagnostics:
there is no package called 'magclass'
--- failed re-building ‘magpie.Rmd’

--- re-building ‘source.Rmd’ using rmarkdown
--- finished re-building ‘source.Rmd’

--- re-building ‘verbose.Rmd’ using rmarkdown
--- finished re-building ‘verbose.Rmd’

--- re-building ‘warn.Rmd’ using rmarkdown
--- finished re-building ‘warn.Rmd’

--- re-building ‘with_regions.Rmd’ using rmarkdown
--- finished re-building ‘with_regions.Rmd’

SUMMARY: processing the following file failed:
  ‘magpie.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘gdxrrw’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gdxdt.Rcheck/00install.out’ for details.
Package required but not available: ‘autoimage’

Packages suggested but not available for checking: 'geoR', 'gstat'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘readr’
Package required but not available: ‘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/GEEaSPU.Rcheck/00install.out’ for details.
Packages required but not available: 'geeM', 'lme4', 'MESS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/geecure.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/geeM.Rcheck/00install.out’ for details.
checkRd: (7) genZcor.Rd:22: \item in \value must have non-empty label
Package required but not available: ‘lme4’

Packages suggested but not available for checking:
  'inferference', 'AER', 'ICSNP', 'ivpack', 'saws'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘phytools’

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: 'survAUC', 'Hmisc', 'quantreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘speedglm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gellipsoid.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gemlog.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘readr’
'LazyData' is specified without a 'data' directory
Running examples in ‘gemma2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calc_XHiY
> ### Title: Calculate XHiY
> ### Aliases: calc_XHiY
> 
> ### ** Examples
> 
> readr::read_tsv(system.file("extdata",
+ "mouse100.pheno.txt",
+ package = "gemma2"),
+ col_names = FALSE) -> pheno
Error in loadNamespace(x) : there is no package called ‘readr’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘compare-with-GEMMAv096.Rmd’ using rmarkdown
Quitting from lines 74-78 (compare-with-GEMMAv096.Rmd) 
Error: processing vignette ‘compare-with-GEMMAv096.Rmd’ failed with diagnostics:
there is no package called 'readr'
--- failed re-building ‘compare-with-GEMMAv096.Rmd’

SUMMARY: processing the following file failed:
  ‘compare-with-GEMMAv096.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘msm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'meta', 'rjags', '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/gen2stage.Rcheck/00install.out’ for details.
Packages required but not available: 'raster', 'gdistance'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gen5helper.Rcheck/00install.out’ for details.
Package required but not available: ‘ClassDiscovery’

Package suggested but not available for checking: ‘Biobase’

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.
Packages required but not available:
  'ggnetwork', 'ggraph', 'phangorn', 'S4Vectors', 'VennDiagram',
  'future.apply', 'ShortRead', 'Biostrings'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'C50'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
genmvnorm: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: ‘genderdata’
Packages required but not available: 'GENEAread', 'changepoint'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GENEAread.Rcheck/00install.out’ for details.
Package required but not available: ‘GENEAread’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘G1DBN’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘longitudinal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Biobase', 'annotate', 'GEOquery', 'R.utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
t1p1: no visible global function definition for ‘var’
t1p1: no visible global function definition for ‘pt’
t1p2: no visible global function definition for ‘pt’
Undefined global functions or variables:
  pt var
Consider adding
  importFrom("stats", "pt", "var")
to your NAMESPACE file.
Rd file 'flexorhtest.Rd':
  \examples lines wider than 100 characters:
          plot(x,y, main="Location and Strong Order Restrictions",cex.axis=1.5, cex.lab=1.5, cex.main=1.5, cex=1.5)

These lines will be truncated in the PDF manual.
Packages required but not available: 'clusterProfiler', 'VennDiagram'

Packages suggested but not available for checking: 'DOSE', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
load.genelist: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  read.delim
Consider adding
  importFrom("utils", "read.delim")
to your NAMESPACE file.
Rd file 'geneListPie-package.Rd':
  \examples lines wider than 100 characters:
     glist<-c("ABCB7","ABCF1","ABHD2","ACAD9","ACIN1","AMOTL1","ANLN","ANXA4","APBA2","APBA3","BAI3","BCLAF1","BEST1")

Rd file 'geneListProfile.Rd':
  \examples lines wider than 100 characters:
     glist<-c("ABCB7","ABCF1","ABHD2","ACAD9","ACIN1","AMOTL1","ANLN","ANXA4","APBA2","APBA3","BAI3","BCLAF1","BEST1")

These lines will be truncated in the PDF manual.
Package required but not available: ‘longitudinal’

Packages suggested but not available for checking: 'graph', 'Rgraphviz'

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
Packages required but not available: 'np', 'meboot'

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: ‘mlogit’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/generalhoslem.Rcheck/00install.out’ for details.
Package required but not available: ‘CVST’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'fields', 'plotly'
'LazyData' is specified without a 'data' directory
Packages required but not available: 'mlr3', 'mlr3learners', 'lmtest'

Package suggested but not available for checking: ‘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/geneSignatureFinder.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘tidyverse’
Packages required but not available:
  'GGEBiplots', 'ggforce', 'pcaMethods', 'rrcov', 'missMDA',
  'calibrate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/genetics.Rcheck/00install.out’ for details.
Packages required but not available:
  'exactextractr', 'spdep', 'raster', 'rgeos'

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: 'doParallel', 'ssdtools'

Packages suggested but not available for checking:
  'gamlss.dist', 'GLDEX', 'sgt', 'sn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/genie.Rcheck/00install.out’ for details.
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘snpStats’

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/GenKern.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/genlasso.Rcheck/00install.out’ for details.
Packages required but not available: 'kinship2', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'distr', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'alabama', 'Hmisc', 'maxLik'

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.
Packages required but not available:
  'S4Vectors', 'GenomicRanges', 'IRanges', 'R.utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'leaflet', 'readr', 'rio'

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'robust', 'SNPRelate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'hierfstat', 'vcfR'

Package suggested but not available for checking: ‘junctions’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/genomeplot.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'SOMbrero', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'reactome.db', 'AnnotationDbi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘snpStats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'gMWT', 'GenomicTools.fileHandler', '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/genoPlotR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GenOrd.Rcheck/00install.out’ for details.
Package required but not available: ‘SKAT’

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.
Packages required but not available: 'diagram', 'quantreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

Package suggested but not available for checking: ‘bestglm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tmvtnorm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'mvmesh', 'geometry', 'SphericalCubature'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
splineAnalyze: no visible global function definition for ‘var’
splineAnalyze: no visible global function definition for ‘par’
splineAnalyze: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines par var
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "var")
to your NAMESPACE file.
Package suggested but not available for checking: ‘geoR’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'spdep', 'reldist', 'future.apply', 'rgeos', 'leaflet', 'plotly',
  'raster', 'rgdal'

Packages suggested but not available for checking:
  'maptools', 'ClustGeo', 'car', 'ggpubr', 'viridis', 'tmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘R.utils’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/geodata.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GeoDE.Rcheck/00install.out’ for details.
Packages required but not available: 'readr', 'rgdal', 'leaflet', 'mapview'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rgeos', 'rgdal', 'maptools'

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
Packages required but not available:
  'raster', 'rgdal', 'rgeos', 'landscapemetrics'

Packages suggested but not available for checking:
  'rasterVis', 'mapdata', 'maptools', 'tidyverse', 'ggmap',
  'factoextra'

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: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggrepel', 'geogrid'

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 suggested but not available for checking:
  'geofacet', 'ggrepel', 'httptest', 'leaflet', 'readr'
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
Package required but not available: ‘rgeos’

Packages suggested but not available for checking: 'rgdal', '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: ‘orthopolynom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mboost’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rgeos’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rgdal’
Running examples in ‘geohashTools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gis_tools
> ### Title: Helpers for interfacing geohashes with sp/sf objects
> ### Aliases: gh_to_sp gh_to_spdf gh_to_spdf.default gh_to_spdf.data.frame
> ###   gh_to_sf gh_covering
> 
> ### ** Examples
> 
>   # get the neighborhood of this geohash in downtown Apia as an sp object
>   downtown = '2jtc5x'
>   apia_nbhd = unlist(gh_neighbors(downtown))
>   apia_sp = gh_to_sp(apia_nbhd)
> 
>   # all geohashes covering a random sampling within Apia:
>   apia_covering = gh_covering(smp <- sp::spsample(apia_sp, 10L, 'random'))
Error in spTransform(x, CRS(CRSobj), ...) : 
  package rgdal is required for spTransform methods
Calls: gh_covering ... <Anonymous> -> <Anonymous> -> spTransform -> spTransform
Execution halted
Packages required but not available: 'rgeos', 'maptools', 'readr'

Packages suggested but not available for checking: 'leaflet', 'RPostgres'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ggmap', 'rasterVis', 'rgdal'
Packages required but not available:
  'tigris', 'readr', 'dataverse', 'censable'

Package suggested but not available for checking: ‘redist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘GEOmap’
Malformed Description field: should contain one or more complete sentences.
Rd file 'fujitopo.Rd':
  \examples lines wider than 100 characters:
     PLOC=list(LON=range(fujitopo$lon), x=range(fujitopo$lon), LAT=range(fujitopo$lat), y=range(fujitopo$lat))

These lines will be truncated in the PDF manual.
Packages required but not available: 'splancs', 'fields'

Package suggested but not available for checking: ‘RFOC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'forecast', 'ForecastCombinations', 'mtsdi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'inlmisc', 'raster', 'spdep'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rgdal', 'raster'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'magic', 'linprog'

Package suggested but not available for checking: ‘R.matlab’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/geomorph.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/geomtextpath.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/geonapi.Rcheck/00install.out’ for details.
Packages required but not available:
  'spatstat.linnet', 'spatstat.geom', 'spatstat.core'

Package suggested but not available for checking: ‘spatstat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rgdal’

Packages suggested but not available for checking:
  'devtools', 'mapview', 'spData', 'tmaptools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RFOC', 'GEOmap'

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:
  'snowfall', 'constrainedKriging', 'fields', 'lmtest', 'quantreg',
  'RandomFields'

Packages suggested but not available for checking: 'gstat', 'multcomp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'splancs', 'RandomFields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
geoscaleBox: no visible global function definition for ‘boxplot’
geoscaleBox: no visible global function definition for ‘par’
geoscaleBox: no visible global function definition for ‘text’
geoscaleBox: no visible global function definition for ‘segments’
geoscaleBox: no visible global function definition for ‘rect’
geoscaleBox: no visible global function definition for ‘rgb’
geoscaleBox: no visible global function definition for ‘polygon’
geoscaleBox: no visible global function definition for ‘points’
geoscaleBox: no visible global function definition for ‘axis’
geoscalePlot: no visible global function definition for ‘par’
geoscalePlot: no visible global function definition for ‘text’
geoscalePlot: no visible global function definition for ‘segments’
geoscalePlot: no visible global function definition for ‘rect’
geoscalePlot: no visible global function definition for ‘rgb’
geoscalePlot: no visible global function definition for ‘points’
geoscalePlot: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis boxplot par points polygon rect rgb segments text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "boxplot", "par", "points", "polygon",
             "rect", "segments", "text")
to your NAMESPACE file.
Package suggested but not available for checking: ‘mapview’
'LazyData' is specified without a 'data' directory
Running examples in ‘geosed-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geo_midpoint
> ### Title: Point of Equidistance to Up to Three Longitude, Latitude Points
> ### Aliases: geo_midpoint
> ### Keywords: circle disk enclosing geo latitude longitude sed smallest
> 
> ### ** Examples
> 
> 
> # Load required packages
> require(mapview)
Loading required package: mapview
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘mapview’
> require(sp)
Loading required package: sp
> 
> # Create sample geo dataset
> sample_coord <-
+    matrix(
+         c(
+             sample(327131680:419648450, 3) / 10000000,
+             sample(-1147301410:-1241938690, 3) / 10000000
+         ),
+         ncol = 2
+     )
> 
> # Generate circumcenter and radius
> gmp <- geo_midpoint(sample_coord)
> 
> # Find distance to circumcenter
> radius <- geo_point_dist(rbind(sample_coord[1, ], gmp))
> 
> # Create 80 sided polygon based on gmp's center and radius
> gmp_poly <- geo_surround_poly(gmp, radius, 80)
> 
> # Join all the points into a single matrix
> bound_poly <- rbind(sample_coord, as.vector(gmp), gmp_poly)
> 
> # Create SpacialPoints object and pass to mapview for visualization
> mapview(
+     SpatialPoints(
+         bound_poly[,c(2, 1)],
+         proj4string = CRS("+proj=longlat +datum=WGS84")
+     )
+ )
Error in mapview(SpatialPoints(bound_poly[, c(2, 1)], proj4string = CRS("+proj=longlat +datum=WGS84"))) : 
  could not find function "mapview"
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘raster’
Running examples in ‘geosphere-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: span
> ### Title: Span of polygons
> ### Aliases: span span,SpatialPolygons-method span,matrix-method
> ### Keywords: methods spatial
> 
> ### ** Examples
> 
> pol <- rbind(c(-180,-20), c(-160,5), c(-60, 0), c(-160,-60), c(-180,-20))
> plot(pol)
> lines(pol)
> # lon and lat span in m
> span(pol, fun=max) 
Loading required namespace: raster
Failed with error:  ‘there is no package called ‘raster’’
Error in .local(x, ...) : 
  you need to install the "raster" package to use this function
Calls: span -> span -> .local -> span -> span -> .local
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘geosphere.Rnw’ using Sweave
Loading required namespace: raster
Failed with error:  ‘there is no package called ‘raster’’

Error: processing vignette ‘geosphere.Rnw’ failed with diagnostics:
 chunk 13 
Error in .local(x, ...) : 
  you need to install the "raster" package to use this function

--- failed re-building ‘geosphere.Rnw’

SUMMARY: processing the following file failed:
  ‘geosphere.Rnw’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'FD', 'StatMatch', 'fields', 'geospt'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gstat', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'spdep', 'rstan'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘cqn’

Packages suggested but not available for checking:
  'DESeq2', 'S4Vectors', 'ChAMP', 'clusterProfiler', 'org.Hs.eg.db',
  'edgeR', 'quantreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Found the following calls to data() loading into the global environment:
File ‘geotools/R/zzz.R’:
  data(fr_geo_rad)
See section ‘Good practice’ in ‘?data’.
Package required but not available: ‘geoR’

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 required but not available: 'ff', 'raster', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggspatial', 'viridis', 'raster', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'readr', 'raster', 'rgeos', 'slippymath', '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/geovol.Rcheck/00install.out’ for details.
Packages required but not available: 'cartography', 'GWmodel', 'raster'

Packages suggested but not available for checking: 'rgdal', 'spdep'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘DescTools’

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: ‘agricolae’

Package suggested but not available for checking: ‘inti’

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: ‘kinship2’

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.
Package suggested but not available for checking: ‘glmnet’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gesso.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/GESTr.Rcheck/00install.out’ for details.
Packages required but not available: 'geeM', 'rsample'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'readr', 'furrr'

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', 'xlsx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
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’

Package suggested but not available for checking: ‘raster’

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: ‘EcoHydRology’

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: ‘readr’

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Skipping vignette re-building
Packages suggested but not available for checking:
  'gstat', 'fda', 'fda.usc', 'spatstat.geom', 'spatstat.core',
  'spatstat.linnet', 'spatstat', 'R.rsp'

VignetteBuilder package required for checking but not installed: ‘R.rsp’
Package required but not available: ‘party’

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: ‘lgarch’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gets.Rcheck/00install.out’ for details.
Package required but not available: ‘RLRsim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Biobase', 'multtest'

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: ‘mboost’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'raster', 'rgdal', 'rgeos', 'rasterVis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘magic’

Package suggested but not available for checking: ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'survminer', 'magic'

Package suggested but not available for checking: ‘condSURV’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘TeachingSampling’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'scatterpie', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cmprsk', 'compound.Cox', 'joint.Cox'

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: 'spatstat', 'spatstat.geom', 'rgr'

Packages suggested but not available for checking:
  'kde1d', 'lmerTest', 'GGally', 'car'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'spatstat', 'spatstat.geom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘SIS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘doSNOW’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggpubr', 'truncreg'

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘ggimage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggallin.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ggrepel’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggalluvial.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'broom.helpers', 'chemometrics', 'ggforce', 'Hmisc', 'labelled',
  'mapproj', 'scagnostics', 'sna'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GGally.Rcheck/00install.out’ for details.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘flexsurv’
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggamma)
  > 
  > test_check("ggamma")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 22 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_ggamma.R:111:2): ggamma equals gengamma.orig from flexsurv ──────
  Error in `dgengamma.orig(x, b, a, k)`: could not find function "dgengamma.orig"
  Backtrace:
      ▆
   1. └─testthat::expect_equal(...) at test_ggamma.R:111:8
   2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
   3.     └─rlang::eval_bare(expr, quo_get_env(quo))
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 22 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gganimate.Rcheck/00install.out’ for details.
Package required but not available: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘corrr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggasym-corrr.Rmd’ using rmarkdown
Quitting from lines 30-34 (ggasym-corrr.Rmd) 
Error: processing vignette ‘ggasym-corrr.Rmd’ failed with diagnostics:
there is no package called 'corrr'
--- failed re-building ‘ggasym-corrr.Rmd’

--- re-building ‘ggasym-stats.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 ‘ggasym-stats.Rmd’

SUMMARY: processing the following file failed:
  ‘ggasym-corrr.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggbeeswarm.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: 'changepoint', 'changepoint.np', 'ecp'

Package suggested but not available for checking: ‘gstat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggcharts.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'readr', 'egg'

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/ggcorrplot.Rcheck/00install.out’ for details.
Package required but not available: ‘gghalves’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggraph', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'rms', 'base.rms'

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggdensity.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘fda’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘labelled’
'LazyData' is specified without a 'data' directory
Running examples in ‘ggeasy-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: easy_labs
> ### Title: Easily add ggplot labels using label attribute of 'data.frame'
> ###   column
> ### Aliases: easy_labs
> 
> ### ** Examples
> 
> 
> iris_labs <- iris
> 
> lbl <- c('Sepal Length', 'Sepal Width', 'Petal Length', 'Petal Width', 'Flower Species')
> 
> labelled::var_label(iris_labs) <- split(lbl,names(iris_labs))
Error in loadNamespace(x) : there is no package called ‘labelled’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [4s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggeasy)
  > 
  > test_check("ggeasy")
  [ FAIL 1 | WARN 16 | SKIP 0 | PASS 432 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-labs.R:2:1): (code run outside of `test_that()`) ────────────────
  <packageNotFoundError/error/condition>
  Error in `library(labelled)`: there is no package called 'labelled'
  Backtrace:
      ▆
   1. └─base::library(labelled) at test-labs.R:2:0
  
  [ FAIL 1 | WARN 16 | SKIP 0 | PASS 432 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘shortcuts.Rmd’ using rmarkdown
Quitting from lines 15-19 (shortcuts.Rmd) 
Error: processing vignette ‘shortcuts.Rmd’ failed with diagnostics:
there is no package called 'labelled'
--- failed re-building ‘shortcuts.Rmd’

--- re-building ‘tests_and_coverage.Rmd’ using rmarkdown
--- finished re-building ‘tests_and_coverage.Rmd’

SUMMARY: processing the following file failed:
  ‘shortcuts.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘ggforce’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggedit.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'AER', 'betareg', 'brms', 'effects', 'gam', 'gamlss', 'gamm4',
  'glmmTMB', 'haven', 'lme4', 'MCMCglmm', 'quantreg', 'rms',
  'rstanarm', 'sjstats', 'survey'
Running examples in ‘ggeffects-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggeffect
> ### Title: Marginal effects, adjusted predictions and estimated marginal
> ###   means from regression models
> ### Aliases: ggeffect ggemmeans ggpredict
> 
> ### ** Examples
> 
> library(sjlabelled)
> data(efc)
> fit <- lm(barthtot ~ c12hour + neg_c_7 + c161sex + c172code, data = efc)
> 
> ggpredict(fit, terms = "c12hour")
# Predicted values of Total score BARTHEL INDEX

c12hour | Predicted |         95% CI
------------------------------------
      0 |     75.44 | [73.26, 77.63]
     20 |     70.38 | [68.56, 72.19]
     45 |     64.05 | [62.39, 65.70]
     65 |     58.98 | [57.16, 60.80]
     85 |     53.91 | [51.71, 56.11]
    105 |     48.85 | [46.15, 51.55]
    125 |     43.78 | [40.52, 47.05]
    170 |     32.38 | [27.73, 37.03]

Adjusted for:
*  neg_c_7 = 11.84
*  c161sex =  1.76
* c172code =  1.97
> ggpredict(fit, terms = c("c12hour", "c172code"))
Error in set_labels_helper(x = .dat, labels = labels, force.labels = force.labels,  : 
  Package 'haven' required for this function. Please install it.
Calls: ggpredict ... .add_labels_to_groupvariable -> <Anonymous> -> set_labels_helper
Execution halted
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'tidyverse', 'RSDA', 'prodlim', 'ggforce', 'ggpubr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘behavr’

Package suggested but not available for checking: ‘zeitgebr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Found the following assignments to the global environment:
File ‘ggExtra/R/ggMarginalGadget.R’:
  assign(plotname, eval(parse(text = origPlot)), envir = .GlobalEnv)
Packages required but not available:
  'FactoMineR', 'widgetframe', 'ggrepel', 'tabxplor'

Package suggested but not available for checking: ‘finalfit’

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: ‘ggrepel’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggfocus.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggforce.Rcheck/00install.out’ for details.
Packages required but not available: 'ggforce', 'labelled'

Packages suggested but not available for checking:
  'mosaic', 'maptools', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'changepoint', 'fGarch', 'forecast', 'ggrepel', 'glmnet', 'mapdata',
  'raster', 'strucchange', 'timeSeries', 'tseries', 'vars', 'xts'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggfortify.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/ggghost.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘mapproj’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gggibbous.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gggrid.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘fitdistrplus’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggh4x.Rcheck/00install.out’ for details.
Package required but not available: ‘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/gghalves.Rcheck/00install.out’ for details.
Package required but not available: ‘hdrcde’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'factoextra', 'ggpubr'

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.
Packages suggested but not available for checking: 'ggh4x', 'tidyverse'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggHoriPlot.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggimage.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gginnards.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggip.Rcheck/00install.out’ for details.
Package required but not available: ‘ppcor’

Packages suggested but not available for checking: 'TH.data', 'ggforce'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggrepel', 'quantreg'
Packages required but not available:
  'doParallel', 'GENEAread', 'unisensR', 'read.gt3x', '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/ggjoy.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/gglorenz.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggmap.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggmatplot.Rcheck/00install.out’ for details.
Package required but not available: ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plotly’
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GGally', 'sna'

Packages suggested but not available for checking:
  'car', 'NetworkToolbox', 'NetworkComparisonTest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'bestglm', 'GGally', 'sna', 'doParallel', 'GGMncv'

Package suggested but not available for checking: ‘qgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'ggrepel'

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 required but not available: ‘graph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GGMridge.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggmr.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GGMselect.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘tidyverse’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggmulti.Rcheck/00install.out’ for details.
Packages required but not available: 'ggrepel', 'sna'

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:
  'ggspatial', 'raster', 'rgeos', 'stars', 'smoothr'

Packages suggested but not available for checking:
  'ggOceanMapsData', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggraph’
Packages required but not available: 'ggforce', '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/ggparallel.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ggrepel’
Running examples in ‘ggparliament-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_parliament_bar
> ### Title: Add a bar showing proportion of seats by party in parliament
> ### Aliases: geom_parliament_bar
> 
> ### ** Examples
> 
> data <- election_data[election_data$country == "USA" &
+ election_data$house == "Representatives" &
+ election_data$year == "2016",]
> usa_data <- parliament_data(election_data = data,
+ type = "semicircle",
+ party_seats = data$seats,
+ parl_rows = 8)
> ggplot2::ggplot(usa_data, ggplot2::aes(x, y, colour = party_long)) +
+ geom_parliament_seats() +
+ geom_parliament_bar(colour, party_long) +
+ ggplot2::scale_colour_manual(values = usa_data$colour, limits = usa_data$party_long)  +
+ theme_ggparliament()
Error in loadNamespace(x) : there is no package called ‘ggrepel’
Calls: +.gg ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package required but not available: ‘partykit’

Packages suggested but not available for checking: 'AER', 'coin', 'TH.data'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'gganimate', 'mapproj', 'readr'
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Hmisc', 'mapproj', 'maptools', 'multcomp', 'quantreg', 'rgeos'
Running examples in ‘ggplot2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coord_map
> ### Title: Map projections
> ### Aliases: coord_map coord_quickmap
> 
> ### ** Examples
> 
> if (require("maps")) {
+ nz <- map_data("nz")
+ # Prepare a map of NZ
+ nzmap <- ggplot(nz, aes(x = long, y = lat, group = group)) +
+   geom_polygon(fill = "white", colour = "black")
+ 
+ # Plot it in cartesian coordinates
+ nzmap
+ }
Loading required package: maps
> 
> if (require("maps")) {
+ # With correct mercator projection
+ nzmap + coord_map()
+ }
Error in mproject(self, grid$x, grid$y, orientation) : 
  The package `mapproj` is required for `coord_map()`
Calls: <Anonymous> ... <Anonymous> -> <Anonymous> -> f -> mproject -> check_installed
Execution halted
Packages required but not available: 'tidyverse', 'editData'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'readr', 'haven'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggimage', 'vcd'
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggplotify.Rmd’ using rmarkdown
Quitting from lines 27-37 (ggplotify.Rmd) 
Error: processing vignette ‘ggplotify.Rmd’ failed with diagnostics:
there is no package called 'vcd'
--- failed re-building ‘ggplotify.Rmd’

SUMMARY: processing the following file failed:
  ‘ggplotify.Rmd’

Error: Vignette re-building failed.
Execution halted
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 required but not available: 'ggpp', 'quantreg'

Packages suggested but not available for checking:
  'ggrepel', 'broom.mixed', 'gginnards'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GGally', 'readr'

Package suggested but not available for checking: ‘nlmixr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘viridis’
'LazyData' is specified without a 'data' directory
Running examples in ‘ggpointdensity-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_pointdensity
> ### Title: A cross between a scatter plot and a 2D density plot
> ### Aliases: geom_pointdensity stat_pointdensity StatPointdensity
> 
> ### ** Examples
> 
> library(ggplot2)
> 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(ggpointdensity)
> 
> # generate some toy data
> dat <- bind_rows(
+   tibble(x = rnorm(7000, sd = 1),
+          y = rnorm(7000, sd = 10),
+          group = "foo"),
+   tibble(x = rnorm(3000, mean = 1, sd = .5),
+          y = rnorm(3000, mean = 7, sd = 5),
+          group = "bar"))
> 
> # plot it with geom_pointdensity()
> ggplot(data = dat, mapping = aes(x = x, y = y)) +
+   geom_pointdensity()
> 
> # adjust the smoothing bandwidth,
> # i.e. the radius around the points
> # in which neighbors are counted
> ggplot(data = dat, mapping = aes(x = x, y = y)) +
+   geom_pointdensity(adjust = .1)
> 
> ggplot(data = dat, mapping = aes(x = x, y = y)) +
+   geom_pointdensity(adjust = 4)
> 
> # I recommend the viridis package
> # for a more useful color scale
> library(viridis)
Error in library(viridis) : there is no package called ‘viridis’
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggpointless.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggpolar.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggpol.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggpolypath.Rcheck/00install.out’ for details.
Package required but not available: ‘xts’

Packages suggested but not available for checking: 'gginnards', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'ggbeeswarm', 'rstatix'
Error(s) in re-building vignettes:
  ...
--- re-building ‘axes.Rmd’ using rmarkdown
--- finished re-building ‘axes.Rmd’

--- re-building ‘colours.Rmd’ using rmarkdown
--- finished re-building ‘colours.Rmd’

--- re-building ‘ggprism.Rmd’ using rmarkdown
--- finished re-building ‘ggprism.Rmd’

--- re-building ‘pvalues.Rmd’ using rmarkdown
Quitting from lines 259-265 (pvalues.Rmd) 
Error: processing vignette ‘pvalues.Rmd’ failed with diagnostics:
there is no package called 'rstatix'
--- failed re-building ‘pvalues.Rmd’

--- re-building ‘themes.Rmd’ using rmarkdown
--- finished re-building ‘themes.Rmd’

SUMMARY: processing the following file failed:
  ‘pvalues.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'ggrepel', 'rstatix'

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:
  'GGally', 'ggbeeswarm', 'ggpmisc', 'ggrepel', 'ggpubr', 'Hmisc',
  'plotly', 'quantreg', 'survminer', 'RPostgres'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggmap’
Package required but not available: ‘randomForestSRC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggforce', 'ggrepel', 'viridis'

Packages suggested but not available for checking: 'seriation', '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/ggraptR.Rcheck/00install.out’ for details.
Packages required but not available: 'mixtools', 'bgmm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggbeeswarm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'devtools', 'ggbeeswarm', 'readr'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggrepel.Rcheck/00install.out’ for details.
Packages required but not available: 'plotly', 'qqplotr'

Packages suggested but not available for checking: 'lme4', 'lmerTest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gRbase', 'CVglasso', 'graph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'egg', 'rms', 'nomogramFormula'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggROC.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘doParallel’
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggseas.Rcheck/00install.out’ for details.
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.
Packages suggested but not available for checking: 'freesurfer', 'devtools'
Error(s) in re-building vignettes:
  ...
--- re-building ‘externalData.Rmd’ using rmarkdown
--- finished re-building ‘externalData.Rmd’

--- re-building ‘freesurfer_files.Rmd’ using rmarkdown
Quitting from lines 11-20 (freesurfer_files.Rmd) 
Error: processing vignette ‘freesurfer_files.Rmd’ failed with diagnostics:
there is no package called 'devtools'
--- failed re-building ‘freesurfer_files.Rmd’

--- re-building ‘ggseg.Rmd’ using rmarkdown
--- finished re-building ‘ggseg.Rmd’

SUMMARY: processing the following file failed:
  ‘freesurfer_files.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘viridis’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggside.Rcheck/00install.out’ for details.
Packages required but not available: 'maptools', 'ggmap'

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: ‘ggmap’
Package suggested but not available for checking: ‘devtools’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘rosm’

Packages suggested but not available for checking:
  'rgdal', 'raster', 'ggrepel', 'stars'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'photobiologyWavebands', 'ggrepel'

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
Packages required but not available: 'ggrepel', 'statsExpressions', 'WRS2'

Packages suggested but not available for checking:
  'afex', 'BayesFactor', 'ggcorrplot', 'gginnards', 'ggside', 'lme4',
  'metaBMA', 'metafor', 'PMCMRplus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggswissmaps.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggtern.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: ‘mapproj’
Running examples in ‘ggthemes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: theme_map
> ### Title: Clean theme for maps
> ### Aliases: theme_map
> 
> ### ** Examples
> 
> library("maps")
> library("ggplot2")
> 
> us <- fortify(map_data("state"), region = "region")
> gg <- ggplot() +
+   geom_map(data  =  us, map = us,
+              aes(x = long, y = lat, map_id = region, group = group),
+              fill = "white", color = "black", size = 0.25) +
+   coord_map("albers", lat0 = 39, lat1 = 45) +
+   theme_map()
Warning: Ignoring unknown aesthetics: x, y
> gg
Error in mproject(self, grid$x, grid$y, orientation) : 
  The package `mapproj` is required for `coord_map()`
Calls: <Anonymous> ... <Anonymous> -> <Anonymous> -> f -> mproject -> check_installed
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggTimeSeries.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘AICcmodavg’
Packages required but not available: 'viridis', 'xlsx'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'RVenn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggvenn.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'ggrepel', 'wordcloud'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ggwordcloud.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'styler', 'readr'
Package required but not available: ‘refund’

Package suggested but not available for checking: ‘GeneralisedCovarianceMeasure’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘CVXR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GHS.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ggraph’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Significantlinks.Rmd’ using rmarkdown
--- finished re-building ‘Significantlinks.Rmd’

--- re-building ‘Tutorial_NRM.Rmd’ using rmarkdown
Quitting from lines 67-71 (Tutorial_NRM.Rmd) 
Error: processing vignette ‘Tutorial_NRM.Rmd’ failed with diagnostics:
there is no package called 'ggraph'
--- failed re-building ‘Tutorial_NRM.Rmd’

--- re-building ‘tutorial.Rmd’ using rmarkdown
--- finished re-building ‘tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘Tutorial_NRM.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ghyp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GibbsACOV.Rcheck/00install.out’ for details.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘gibbs.met/R/firstlib.R’:
  .First.lib calls:
    cat("Naive Gibbs Sampling with Metropolis steps(gibbs.met) loaded\n",     "COPYRIGHT 2008 (c) Longhai Li (http://math.usask.ca/~longhai)\n",     "Type ?begin.gibbs.met for help to this package\n", sep = "")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in ‘?.onAttach’.

met_gaussian : one_transition: no visible global function definition
  for ‘rnorm’
met_gaussian : one_transition: no visible global function definition
  for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘mc_mvn_closemix.eps’ ‘mc_mvn_farmix_met.eps’ ‘mc_mvn_lowcor.eps’
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.
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'qgraph', 'MIIVsem', 'imputeTS'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘easycsv’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'zyp'

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
Unknown package ‘IC2’ in Rd xrefs
Packages required but not available: 'raster', '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: ‘eurostat’
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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gitear.Rcheck/00install.out’ for details.
Package required but not available: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘alabama’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'quantreg', 'MCMCpack'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'magic', 'survey', 'gamlss.dist', 'Rmpfr', 'scam', 'distrEx', 'ismev'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘seqinr’

Packages suggested but not available for checking:
  'rtracklayer', 'GenomicRanges', 'BSgenome',
  'BSgenome.Hsapiens.UCSC.hg18.masked',
  'BSgenome.Hsapiens.UCSC.hg19.masked', 'Biostrings', 'GenomeInfoDb',
  'IRanges', 'S4Vectors'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Ecdat’

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: ‘glmnet’

Package suggested but not available for checking: ‘doMC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
fptcdf: no visible global function definition for ‘dnorm’
fptcdf: no visible global function definition for ‘pnorm’
fptpdf: no visible global function definition for ‘pnorm’
fptpdf: no visible global function definition for ‘dnorm’
lba: no visible global function definition for ‘as.formula’
lba: no visible global function definition for ‘model.frame’
lba : logl: no visible global function definition for ‘head’
lba: no visible global function definition for ‘optim’
pmod: no visible global function definition for ‘model.frame’
pmod: no visible global function definition for ‘model.matrix’
rlba: no visible global function definition for ‘pnorm’
rlba: no visible global function definition for ‘rnorm’
rlba: no visible global function definition for ‘runif’
tablba: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula dnorm head model.frame model.matrix optim pnorm rnorm
  runif
Consider adding
  importFrom("stats", "as.formula", "dnorm", "model.frame",
             "model.matrix", "optim", "pnorm", "rnorm", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
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.
Package suggested but not available for checking: ‘gclus’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gllvm.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GLMaSPU.Rcheck/00install.out’ for details.
Package required but not available: ‘emplik’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'caret', 'gam'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'lme4', 'partykit'

Package suggested but not available for checking: ‘vcd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'lme4', 'lmerTest', 'gam', 'multcomp'
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [18s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(glmglrt)
  > 
  > test_check("glmglrt")
  [ FAIL 1 | WARN 54 | SKIP 0 | PASS 241 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-confint_contrast.R:141:2): confint_contrast with Wald's formula on many other models ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'lmerTest'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-confint_contrast.R:141:8
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base withOneRestart(expr, restarts[[1L]])
   4.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 54 | SKIP 0 | PASS 241 ]
  Error: Test failures
  Execution halted
Packages suggested but not available for checking:
  'multcomp', 'effects', 'DHARMa'
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘mlmRev’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'broom.mixed', 'rstan'

Package suggested but not available for checking: ‘viridis’

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: 'lme4', 'rstan'

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 required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'car', 'gghalves', 'ggpubr', 'lme4', 'plotly'

Package suggested but not available for checking: ‘edgeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Packages suggested but not available for checking:
  'mlmRev', 'car', 'DHARMa', 'multcomp', 'effects', 'dotwhisker',
  'broom.mixed'

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/glmnet.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: ‘glmnet’

Package suggested but not available for checking: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'effects', 'AER', 'lme4', 'lmtest', 'censReg', 'plm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘glmpath’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/glmpath.Rcheck/00install.out’ for details.
Packages required but not available: 'mlogit', 'survey', 'AER'

Package suggested but not available for checking: ‘devtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘cplm’

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: ‘Rfast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'doParallel', 'caret'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'partykit', 'caret'

Package suggested but not available for checking: ‘FactoMineR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/glmulti.Rcheck/00install.out’ for details.
Packages required but not available: 'glmnet', 'brglm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lmtest’

Package suggested but not available for checking: ‘AER’

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.
Package required but not available: ‘sybil’

Package suggested but not available for checking: ‘cplexAPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
CreateFormula: no visible global function definition for ‘as.formula’
GeneratePvalues: no visible binding for global variable ‘binomial’
globalARTP: no visible binding for global variable ‘binomial’
globalFisher: no visible binding for global variable ‘binomial’
globalFisher: no visible global function definition for ‘pchisq’
globalSimes: no visible binding for global variable ‘binomial’
pvalFmla: no visible binding for global variable ‘binomial’
pvalFmla: no visible global function definition for ‘glm’
pvalFmla: no visible global function definition for ‘anova’
runPermut: no visible binding for global variable ‘binomial’
runPvalues: no visible binding for global variable ‘binomial’
Undefined global functions or variables:
  anova as.formula binomial glm pchisq
Consider adding
  importFrom("stats", "anova", "as.formula", "binomial", "glm", "pchisq")
to your NAMESPACE file.
Packages required but not available:
  'spatstat.random', 'spatstat.core', 'spatstat.geom'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Packages suggested but not available for checking:
  'strucchange', 'fxregime'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/glogis.Rcheck/00install.out’ for details.
Package required but not available: ‘tmap’

Packages suggested but not available for checking:
  'mapedit', 'plotly', '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/glow.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mvSLOUCH’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GLSME.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'R.utils', 'RSQLite'
Error(s) in re-building vignettes:
  ...
--- re-building ‘engines.Rmd’ using rmarkdown
Quitting from lines 55-58 (engines.Rmd) 
Error: processing vignette ‘engines.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 ‘engines.Rmd’

--- re-building ‘speed.Rmd’ using rmarkdown
--- finished re-building ‘speed.Rmd’

--- re-building ‘transformers.Rmd’ using rmarkdown
hello!
Loading required package: emo
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'emo'
--- finished re-building ‘transformers.Rmd’

SUMMARY: processing the following file failed:
  ‘engines.Rmd’

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:
  'maptools', 'coin', 'DescTools', 'dismo', 'ggrepel', 'Hmisc',
  'InPosition', 'raster', 'RcmdrMisc', 'rgdal', 'rgeos',
  'spatstat.geom', 'spatstat.core', 'spatstat.random'

Package suggested but not available for checking: ‘gdistance’

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: ‘gRbase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Hmisc’
Error(s) in re-building vignettes:
  ...
--- re-building ‘usage-example-general-model.Rmd’ using rmarkdown
--- finished re-building ‘usage-example-general-model.Rmd’

--- re-building ‘usage-example-special-model.Rmd’ using rmarkdown
--- finished re-building ‘usage-example-special-model.Rmd’

--- re-building ‘usage-shiny-graphical-interface.Rmd’ using rmarkdown
--- finished re-building ‘usage-shiny-graphical-interface.Rmd’

--- re-building ‘GMCM-JStatSoft.Rnw’ using knitr
Quitting from lines 128-128 (GMCM-JStatSoft.Rnw) 
Error: processing vignette ‘GMCM-JStatSoft.Rnw’ failed with diagnostics:
there is no package called 'Hmisc'
--- failed re-building ‘GMCM-JStatSoft.Rnw’

SUMMARY: processing the following file failed:
  ‘GMCM-JStatSoft.Rnw’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'multcomp', 'xlsxjars'

Packages suggested but not available for checking:
  'Deducer', 'graph', 'mutoss', 'coin'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RMySQL’

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gmeta.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘gstat’

Package suggested but not available for checking: ‘DescTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (7) param_learn.Rd:47-48: \item in \value must have non-empty label
checkRd: (7) param_learn.Rd:49-52: \item in \value must have non-empty label
checkRd: (7) struct_learn.Rd:66-67: \item in \value must have non-empty label
checkRd: (7) struct_learn.Rd:68-71: \item in \value must have non-empty label
Packages required but not available: 'forestplot', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Packages required but not available: 'SeqArray', 'SeqVarTools'

Package suggested but not available for checking: ‘doMC’

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.
Packages suggested but not available for checking: 'car', 'timeSeries'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gmm.Rcheck/00install.out’ for details.
Packages required but not available: 'maxLik', 'msm', 'mlogit'

Packages suggested but not available for checking:
  'AER', 'lmtest', 'car', 'memisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘lme4’
checkRd: (7) estimable.Rd:97: invalid email address: bxc\@novonordisk.com
Packages required but not available: 'ggrepel', 'geometry', 'Rfast'

Packages suggested but not available for checking: 'tidyverse', 'webshot2'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mvp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rmpfr’
'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’
Package required but not available: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'magclass', 'qgraph'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gMWT.Rcheck/00install.out’ for details.
Packages required but not available:
  'PerformanceAnalytics', 'nonlinearTseries', 'fitdistrplus', 'tseries'

Packages suggested but not available for checking: 'xts', 'quantmod'

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.
Package required but not available: ‘alabama’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ismev’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gnlm.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘vcdExtra’
Package required but not available: ‘qrng’

Packages suggested but not available for checking: 'nvmix', 'qrmdata'

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: ‘devtools’
Package required but not available: ‘capushe’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gnumeric.Rcheck/00install.out’ for details.
Package required but not available: ‘Rmpfr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'vegan', 'ggrepel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'vegan', 'fields', 'Hmisc'

Packages suggested but not available for checking:
  'vegdata', 'BiodiversityR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rrpack', 'glmnet'

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 required but not available: ‘epiR’

Package suggested but not available for checking: ‘mlogit’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fitdistrplus', 'survsim'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doSNOW', 'R.utils', 'yarrr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fda.usc', 'glmnet', 'ks'

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/GoFKernel.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'fitdistrplus', 'sn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GANPA', 'WGCNA'

Packages suggested but not available for checking: 'GANPA', 'WGCNA'

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/goldilocks.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: ‘car’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘GoodmanKruskal.Rmd’ using rmarkdown
Loading required package: GoodmanKruskal
Loading required package: MASS
Loading required package: car
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'car'
Quitting from lines 148-151 (GoodmanKruskal.Rmd) 
Error: processing vignette ‘GoodmanKruskal.Rmd’ failed with diagnostics:
object ‘Greene’ not found
--- failed re-building ‘GoodmanKruskal.Rmd’

SUMMARY: processing the following file failed:
  ‘GoodmanKruskal.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘maxLik’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Package required but not available: ‘jose’

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
'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/GoogleKnowledgeGraphR.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘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
Package suggested but not available for checking: ‘readr’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GOplot.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GORCure.Rcheck/00install.out’ for details.
Package required but not available: ‘lme4’

Package suggested but not available for checking: ‘restriktor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/goric.Rcheck/00install.out’ for details.
Packages required but not available:
  'BradleyTerry2', 'ggparty', 'partykit', 'PlackettLuce'

Package suggested but not available for checking: ‘psychotree’

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
Malformed Description field: should contain one or more complete sentences.
Packages required but not available:
  'GO.db', 'ggraph', 'biomaRt', 'annotate'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'barcode', 'vcd'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'randtoolbox', 'KrigInv', 'ks'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gpboost.Rcheck/00install.out’ for details.
Packages required but not available: 'ltm', 'caret', 'mirt'

Package suggested but not available for checking: ‘gvcm.cat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
.r1: no visible global function definition for ‘cor’
.r2: no visible global function definition for ‘cor’
rgp: no visible global function definition for ‘runif’
rgp: no visible global function definition for ‘rexp’
Undefined global functions or variables:
  cor rexp runif
Consider adding
  importFrom("stats", "cor", "rexp", "runif")
to your NAMESPACE file.
Packages required but not available: 'fields', 'fda', 'fda.usc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'GPareto', 'KrigInv'

Package suggested but not available for checking: ‘DiceOptim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'fields', 'maptools'
Running examples in ‘GpGp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: L_mult
> ### Title: Multiply approximate Cholesky by a vector
> ### Aliases: L_mult
> 
> ### ** Examples
> 
> n <- 2000
> locs <- matrix( runif(2*n), n, 2 )
> covparms <- c(2, 0.2, 0.75, 0.1)
> ord <- order_maxmin(locs)
> NNarray <- find_ordered_nn(locs,20)
Error in loadNamespace(x) : there is no package called ‘fields’
Calls: find_ordered_nn ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
'LazyData' is specified without a 'data' directory
Package required but not available: ‘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/GPLTR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gpmap.Rcheck/00install.out’ for details.
Packages required but not available: 'randtoolbox', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘GPoM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GPoM.Rcheck/00install.out’ for details.
Package required but not available: ‘rstan’

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: ‘rstan’

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: ‘nbpMatching’

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/GPvam.Rcheck/00install.out’ for details.
Package required but not available: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘seqinr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'glmnet', 'scalreg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'car', 'Hmisc', 'lme4', 'lmerTest'

Package suggested but not available for checking: ‘pbkrtest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'furrr'

Packages suggested but not available for checking:
  'landscapetools', 'rgdal'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'gRbase', 'graph', 'Rgraphviz'

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: ‘rgeos’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘GRANCore’

Package suggested but not available for checking: ‘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/GRANCore.Rcheck/00install.out’ for details.
Packages required but not available: 'vars', '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/granovaGG.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
Packages required but not available:
  'ggpubr', 'Hmisc', 'agricolae', 'PairedData'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gRapfa.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'adegenet', 'spatstat.geom', 'spatstat.linnet', 'vegan', 'pegas',
  'diveRsity', 'gdistance', 'raster'

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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages required but not available: 'glmnet', '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/graphkernels.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'ggraph', 'uwot'
Running examples in ‘graphlayouts-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: annotate_circle
> ### Title: annotate concentric circles
> ### Aliases: annotate_circle
> 
> ### ** Examples
> 
> library(igraph)

Attaching package: ‘igraph’

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

> library(ggraph)
Error in library(ggraph) : there is no package called ‘ggraph’
Execution halted
Package required but not available: ‘FactoMineR’

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’
Packages required but not available: 'magicaxis', 'raster', 'docore'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GrassmannOptim.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'gamm4', 'lme4', 'scam'
Running ‘test-all.R’ [3s/6s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > ## Test `gratia` using the `testthat` package
  > 
  > ## Setup
  > library("testthat")
  > 
  > ## Runs the tests in tests/testthat
  > test_check("gratia")
  Loading required package: gratia
  Loading required package: nlme
  This is mgcv 1.8-40. For overview type 'help("mgcv-package")'.
  Error in library("gamm4") : there is no package called 'gamm4'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Packages required but not available: 'quadmesh', 'raster'

Packages suggested but not available for checking:
  'devtools', 'maptools', 'oce', 'rgdal', 'rworldmap', 'spex'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'doRNG', 'forecast', 'GA', 'tsfeatures'

Packages suggested but not available for checking: 'feasts', 'fGarch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘forecast’

Packages suggested but not available for checking:
  'future.apply', 'ggrepel', 'survey', 'taxstats', 'taxstats1516',
  'viridis'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘readr’
Packages required but not available: 'lmtest', 'censReg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'graph', 'RBGL', '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/GRCdata.Rcheck/00install.out’ for details.
Package required but not available: ‘gRbase’

Packages suggested but not available for checking: 'Rgraphviz', 'RBGL'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'ggpubr', 'ggrepel', 'viridis'

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: ‘cba’

Package suggested but not available for checking: ‘ggraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GreedyExperimentalDesignJARs.Rcheck/00install.out’ for details.
Packages required but not available:
  'GreedyExperimentalDesignJARs', 'nbpMatching', 'survey'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘swirlify’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'hydroGOF', 'FME', 'tmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'forestplot', 'Gmisc', 'Hmisc', 'rms', 'Epi'

Package suggested but not available for checking: ‘cmprsk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gremlin.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: 'Hmisc', 'rms', 'latticeExtra'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'cramer', 'DiagrammeR', 'fields', 'MCMCpack', 'tidyverse',
  'truncdist'
Packages suggested but not available for checking:
  'smooth', 'doMC', 'doParallel'

Package which this enhances but not available for checking: ‘vars’
Packages required but not available: 'Hmisc', 'survAUC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lmtest’

Package suggested but not available for checking: ‘DiagrammeR’

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: 'graph', 'gridGraphviz'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘egg’
Packages required but not available: 'graph', 'Rgraphviz'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fossil’

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/grImport.Rcheck/00install.out’ for details.
Package required but not available: ‘car’

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.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘msm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cvTools', '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 suggested but not available for checking: ‘phangorn’
Package required but not available: ‘arules’

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: 'hydroGOF', 'lmerTest'
Error(s) in re-building vignettes:
  ...
--- re-building ‘automatic_groups_with_groupdata2.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 ‘automatic_groups_with_groupdata2.Rmd’

--- re-building ‘cross-validation_with_groupdata2.Rmd’ using rmarkdown
Quitting from lines 92-125 (cross-validation_with_groupdata2.Rmd) 
Error: processing vignette ‘cross-validation_with_groupdata2.Rmd’ failed with diagnostics:
there is no package called 'lmerTest'
--- failed re-building ‘cross-validation_with_groupdata2.Rmd’

--- re-building ‘description_of_groupdata2.Rmd’ using rmarkdown
--- finished re-building ‘description_of_groupdata2.Rmd’

--- re-building ‘introduction_to_groupdata2.Rmd’ using rmarkdown
--- finished re-building ‘introduction_to_groupdata2.Rmd’

--- re-building ‘time_series_with_groupdata2.Rmd’ using rmarkdown
Don't know how to automatically pick scale for object of type ts. Defaulting to continuous.
--- finished re-building ‘time_series_with_groupdata2.Rmd’

SUMMARY: processing the following file failed:
  ‘cross-validation_with_groupdata2.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘doParallel’

Package suggested but not available for checking: ‘snplist’

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: ‘rjags’

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/growfunctions.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
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: ‘clime’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘FME’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/growth.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/grpCox.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/grplassocat.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [10s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(grpSLOPE)
  > 
  > test_check("grpSLOPE")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 321 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_grpSLOPE.R:24:3): when the groups are consecutive blocks ──────
  result$c not equal to `sol.c`.
  2/10 mismatches (average diff: 13.3)
  [3]  2.98 - 17.0 == -14.0
  [4] 17.46 -  4.9 ==  12.6
  ── Failure (test_grpSLOPE.R:328:3): when the groups are consecutive blocks ─────
  result$c not equal to `sol.c`.
  2/10 mismatches (average diff: 13.3)
  [3]  2.98 - 17.0 == -14.0
  [4] 17.46 -  4.9 ==  12.6
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 321 ]
  Error: Test failures
  Execution halted
Found the following files/directories:
  ‘p1_20up-vs-p2_25up_in_str1.txt’ ‘p1_20up-vs-p2_25up_in_str2.txt’
  ‘p2_25up-vs-p1_20up_in_str1.txt’ ‘p2_25up-vs-p1_20up_in_str2.txt’
  ‘s0_20up.txt’ ‘s0_30up.txt’ ‘s0_f2up.txt’ ‘strs.vec_01mx.txt’
  ‘strs.vec_02mx.txt’ ‘strs.vec_03mx.txt’ ‘strs.vec_04mx.txt’
  ‘strs.vec_05mx.txt’ ‘strs.vec_06mx.txt’ ‘strs.vec_30up.txt’
  ‘strs.vec_50up.txt’ ‘strs.vec_f2up.txt’ ‘uni_p1_20up-p2_25up.txt’
Packages required but not available: 'glmnet', 'RPtests'

Package suggested but not available for checking: ‘xyz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘FMD mag discontinuities_disc.png’ ‘FMD mag
  discontinuities_disc1.res’ ‘FMD mag discontinuities_disc2.res’
  ‘IDYLLWILD_bvmed.png’ ‘IDYLLWILD_fig.png’ ‘Schuster's
  diagram_schu.png’ ‘hour.res’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/grt.Rcheck/00install.out’ for details.
Package required but not available: ‘edgeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
.gsa.assignGATKTableToEnvironment: 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: ‘gsDesign’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'doSNOW'

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/GSDA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gsDesign.Rcheck/00install.out’ for details.
Package required but not available: ‘R.utils’

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.
Package required but not available: ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rrcov', 'cellWise'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'Hmisc', 'MCMCpack'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘readr’
Package suggested but not available for checking: ‘imager’
checkRd: (7) mexihat.Rd:43: invalid email address: <sylvain.pelissier@gmail.com>
checkRd: (7) morlet.Rd:38: invalid email address: <sylvain.pelissier@gmail.com>
checkRd: (7) nuttallwin.Rd:46: invalid email address: <sylvain.pelissier@gmail.com>
checkRd: (7) pburg.Rd:89: invalid email address: pvl@mecheng.adelaide.edu.au>
checkRd: (7) pyulear.Rd:75: invalid email address: pvl@mecheng.adelaide.edu.au>
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘Introduction.Rmd’
Malformed Description field: should contain one or more complete sentences.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GSM.Rcheck/00install.out’ for details.
Package required but not available: ‘R.utils’

Package suggested but not available for checking: ‘mapproj’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
ldSecControl: no visible global function definition for ‘bounds’
ldSecondaryBoundary: no visible global function definition for ‘bounds’
secondaryBoundaryVecLD: no visible global function definition for
  ‘bounds’
Undefined global functions or variables:
  bounds
'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: ‘xts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘spacetime’

Packages suggested but not available for checking:
  'fields', 'mapdata', 'maptools', 'rgdal', 'rgeos', 'stars', 'xts',
  'raster', 'future.apply'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘quantreg’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gsubfn.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GsymPoint.Rcheck/00install.out’ for details.
Packages required but not available: 'GGally', 'doRNG', 'doParallel', 'lfe'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘interval’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gte.Rcheck/00install.out’ for details.
Packages required but not available: 'furrr', 'readr'

Package suggested but not available for checking: ‘bit64’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'alphahull', 'leafem', 'mapview'
Package required but not available: ‘lme4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'car', 'SGP', 'taxize'
Found the following possibly unsafe calls:
File ‘gtools/R/unByteCode.R’:
  unlockBinding(name, env = env)
checkRd: (7) checkRVersion.Rd:46: invalid email address: gregory.warnes@rochester.edu>
Package required but not available: ‘hts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘broom.helpers’

Packages suggested but not available for checking:
  'broom.mixed', 'car', 'GGally', 'Hmisc', 'lme4', 'survey',
  'tidycmprsk'

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
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 195-198 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
there is no package called 'readr'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'spdep', 'adegraphics', 'adespatial', 'maptools', 'car', 'ggrepel',
  'heplots', 'candisc'
Running examples in ‘Guerry-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Guerry
> ### Title: Data from A.-M. Guerry, "Essay on the Moral Statistics of
> ###   France"
> ### Aliases: Guerry
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(car)
Error in library(car) : there is no package called ‘car’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MultiSpat.Rmd’ using rmarkdown
Quitting from lines 36-42 (MultiSpat.Rmd) 
Error: processing vignette ‘MultiSpat.Rmd’ failed with diagnostics:
there is no package called 'adegraphics'
--- failed re-building ‘MultiSpat.Rmd’

SUMMARY: processing the following file failed:
  ‘MultiSpat.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package vignette with placeholder title ‘Vignette Title’:
  ‘GuessCompx.Rmd’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GUIDE.Rcheck/00install.out’ for details.
Packages required but not available: 'Rgraphviz', 'graph'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘hydroGOF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'vegan', 'ggrepel', 'modeest'

Package suggested but not available for checking: ‘ggpubr’

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 suggested but not available for checking:
  'adaptMCMC', 'xlsx', 'drc'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GUTS.Rcheck/00install.out’ for details.
Packages required but not available:
  'vars', 'xts', 'lmtest', 'strucchange', 'tsDyn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gvcm.cat.Rcheck/00install.out’ for details.
Packages required but not available: 'eda4treeR', 'lme4'

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.
Packages required but not available: 'Biobase', 'snpStats'

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.
Packages required but not available: 'mombf', 'speedglm'

Package suggested but not available for checking: ‘glmnet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'RSQLite', 'R.utils'

Package suggested but not available for checking: ‘xlsx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘httptest’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(gwasrapidd)
  > 
  > test_check("gwasrapidd")
  Error in library(httptest) : there is no package called 'httptest'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Packages required but not available:
  'leaflet', 'leaflet.extras', 'nhdplusTools', 'elevatr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'maptools', 'spData', 'spdep', 'GWmodel', 'spgwr', 'glogis'

Package suggested but not available for checking: ‘rgdal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fGarch', 'doParallel', 'Renext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'rgdal', 'rgeos'
normalweight: no visible binding for global variable ‘NW_above’
normalweight: no visible binding for global variable ‘NW_below’
obese: no visible global function definition for ‘data’
obese: no visible binding for global variable ‘OB_above’
obese: no visible binding for global variable ‘OB_below’
overweight: no visible global function definition for ‘data’
overweight: no visible binding for global variable ‘OW_above’
overweight: no visible binding for global variable ‘OW_below’
Undefined global functions or variables:
  NW_above NW_below OB_above OB_below OW_above OW_below data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘GWG/R/obese.R’:
  data(OB_above)
  data(OB_below)
File ‘GWG/R/overweight.R’:
  data(OW_above)
  data(OW_below)
See section ‘Good practice’ in ‘?data’.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gWidgets2.Rcheck/00install.out’ for details.
Package required but not available: ‘gWidgets2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'doParallel', 'spgwr', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'maptools', 'spatialreg', 'spacetime', 'spdep'

Packages suggested but not available for checking:
  'mvoutlier', 'gstat', 'spData'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘spData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotly', 'viridis', 'leaflet'

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', 'GWmodel', 'lmtest', 'plm'

Packages suggested but not available for checking: 'rgeos', 'tmap'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'plotROC', 'future.apply', 'ggrepel'

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: ‘fields’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geometry', 'raster', 'splancs'

Package suggested but not available for checking: ‘RSQLite’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘testdata1.txt’ ‘testdata2.txt’ ‘testdata3.txt’
Package required but not available: ‘prodlim’

Package suggested but not available for checking: ‘BinaryDosage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GxMestimator: no visible global function definition for ‘na.omit’
initialization_chol: no visible global function definition for ‘cov’
initialization_corr: no visible global function definition for ‘cov’
initialization_nlmain: no visible global function definition for
  ‘lm.fit’
print.summaryGxMclass: no visible global function definition for
  ‘pnorm’
print.summaryGxMclass: no visible global function definition for
  ‘printCoefmat’
Undefined global functions or variables:
  cov lm.fit na.omit pnorm printCoefmat
Consider adding
  importFrom("stats", "cov", "lm.fit", "na.omit", "pnorm",
             "printCoefmat")
to your NAMESPACE file.
checkRd: (7) GxM.Rd:33: \item in \describe must have non-empty label
checkRd: (7) GxM.Rd:35: \item in \describe must have non-empty label
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Morpho', 'cxhull'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'bit64', 'plot3Drgl', 'plotly'
Package required but not available: ‘wavethresh’

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
Package required but not available: ‘future.apply’

Package suggested but not available for checking: ‘httptest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘future.apply’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/HAC.Rcheck/00install.out’ for details.
Package required but not available: ‘pegas’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'gsubfn', '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/HadoopStreaming.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘vegan’
Error(s) in re-building vignettes:
  ...
--- re-building ‘betadiversity.Rmd’ using rmarkdown
Quitting from lines 225-243 (betadiversity.Rmd) 
Error: processing vignette ‘betadiversity.Rmd’ failed with diagnostics:
object ‘pathotype.disp.TukeyHSD’ not found
--- failed re-building ‘betadiversity.Rmd’

--- re-building ‘hagis.Rmd’ using rmarkdown
--- finished re-building ‘hagis.Rmd’

SUMMARY: processing the following file failed:
  ‘betadiversity.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 required but not available: 'origami', 'glmnet'

Package suggested but not available for checking: ‘SuperLearner’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'future.apply', 'hal9001', 'origami', 'rsample'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'lme4', 'nbpMatching', 'lmerTest'
Suggests orphaned package: ‘bibtex’
Packages suggested but not available for checking: 'devtools', 'mda'
Error(s) in re-building vignettes:
  ...
--- re-building ‘consensus_auc.Rnw’ using Sweave

Error: processing vignette ‘consensus_auc.Rnw’ failed with diagnostics:
 chunk 5 
Error in library(mda) : there is no package called ‘mda’

--- failed re-building ‘consensus_auc.Rnw’

SUMMARY: processing the following file failed:
  ‘consensus_auc.Rnw’

Error: Vignette re-building failed.
Execution halted
EMvar: no visible global function definition for ‘model.matrix’
RecodeHaplos: no visible global function definition for ‘na.omit’
RecodeHaplos: no visible global function definition for ‘tail’
anova.hapassoc: no visible global function definition for ‘pchisq’
handleMissings: no visible global function definition for ‘na.omit’
hapassoc: no visible global function definition for ‘binomial’
hapassoc: no visible global function definition for ‘formula’
hapassoc: no visible global function definition for ‘glm’
hapassoc : <anonymous>: no visible global function definition for ‘glm’
hapassoc: no visible global function definition for ‘model.frame’
hapassoc: no visible global function definition for ‘model.matrix’
hapassoc: no visible binding for global variable ‘contrasts’
hapassoc: no visible global function definition for ‘glm.control’
hapassoc : <anonymous>: no visible global function definition for
  ‘glm.control’
probY: no visible global function definition for ‘dbinom’
probY: no visible global function definition for ‘dpois’
probY: no visible global function definition for ‘dnorm’
probY: no visible global function definition for ‘dgamma’
summary.hapassoc: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  binomial contrasts dbinom dgamma dnorm dpois formula glm glm.control
  model.frame model.matrix na.omit pchisq tail
Consider adding
  importFrom("stats", "binomial", "contrasts", "dbinom", "dgamma",
             "dnorm", "dpois", "formula", "glm", "glm.control",
             "model.frame", "model.matrix", "na.omit", "pchisq")
  importFrom("utils", "tail")
to your NAMESPACE file.
allele.marq: no visible global function definition for ‘na.omit’
depart.LDL: no visible global function definition for ‘aov’
freq.all: no visible global function definition for ‘na.omit’
hapim.LD.add: no visible global function definition for ‘optim’
hapim.LDL.add: no visible global function definition for ‘optim’
obj.haplomax.HS.add: no visible global function definition for ‘aov’
obj.haplomax.add: no visible global function definition for ‘aov’
vrais.LD.add: no visible global function definition for ‘dnorm’
vrais.LDL.add.pere: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  aov dnorm na.omit optim
Consider adding
  importFrom("stats", "aov", "dnorm", "na.omit", "optim")
to your NAMESPACE file.
Package required but not available: ‘ff’

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.
Package suggested but not available for checking: ‘pedigree’
AssignQTL : <anonymous>: no visible global function definition for
  ‘rgamma’
AssignSingleQTL: no visible global function definition for ‘rgamma’
ListQTL : <anonymous>: no visible global function definition for
  ‘rgamma’
SampleBaseHaplotype: no visible global function definition for ‘runif’
SampleHaplotype: no visible global function definition for ‘rpois’
SampleHaplotype: no visible global function definition for ‘runif’
SampleHaplotype: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  rbinom rgamma rpois runif
Consider adding
  importFrom("stats", "rbinom", "rgamma", "rpois", "runif")
to your NAMESPACE file.
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.
Packages required but not available: 'sna', 'phangorn'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stars’

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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hapsim.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'devtools', 'recipes'
Running examples in ‘hardhat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: default_recipe_blueprint
> ### Title: Default recipe blueprint
> ### Aliases: default_recipe_blueprint mold.recipe
> 
> ### ** Examples
> 
> library(recipes)
Error in library(recipes) : there is no package called ‘recipes’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘forge.Rmd’ using rmarkdown
Quitting from lines 165-173 (forge.Rmd) 
Error: processing vignette ‘forge.Rmd’ failed with diagnostics:
there is no package called 'recipes'
--- failed re-building ‘forge.Rmd’

--- re-building ‘mold.Rmd’ using rmarkdown
Quitting from lines 215-226 (mold.Rmd) 
Error: processing vignette ‘mold.Rmd’ failed with diagnostics:
there is no package called 'recipes'
--- failed re-building ‘mold.Rmd’

--- re-building ‘package.Rmd’ using rmarkdown
Quitting from lines 280-292 (package.Rmd) 
Error: processing vignette ‘package.Rmd’ failed with diagnostics:
there is no package called 'recipes'
--- failed re-building ‘package.Rmd’

SUMMARY: processing the following files failed:
  ‘forge.Rmd’ ‘mold.Rmd’ ‘package.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/HardyWeinberg.Rcheck/00install.out’ for details.
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/harmonicmeanp.Rcheck/00install.out’ for details.
Package required but not available: ‘irlba’

Package suggested but not available for checking: ‘Seurat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Running examples in ‘HARtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: readHAR
> ### Title: Read HAR objects
> ### Aliases: readHAR
> 
> ### ** Examples
> 
> har <- readHAR(system.file(package = "HARtools",
+                         "exdata", "google.com.har"))
Error in is.list(x) && (required %in% names(x)) : 
  'length = 3' in coercion to 'logical(1)'
Calls: readHAR ... tryCatchOne -> doTryCatch -> eval -> eval -> contains_required
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Basic_use.Rmd’ using rmarkdown
Quitting from lines 50-54 (Basic_use.Rmd) 
Error: processing vignette ‘Basic_use.Rmd’ failed with diagnostics:
'length = 3' in coercion to 'logical(1)'
--- failed re-building ‘Basic_use.Rmd’

SUMMARY: processing the following file failed:
  ‘Basic_use.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Packages required but not available: 'Rgraphviz', 'graph'

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/hawkesbow.Rcheck/00install.out’ for details.
Package required but not available: ‘ahaz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
extract_hazus_functions: no visible global function definition for
  ‘data’
Undefined global functions or variables:
  data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
Package required but not available: ‘rstan’

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hbim.Rcheck/00install.out’ for details.
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘survey’
Package required but not available: ‘fBasics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
PoincarePlot: no visible global function definition for ‘lines’
PoincarePlot: no visible global function definition for ‘lowess’
hctest: no visible global function definition for ‘cor.test’
rdplot: no visible global function definition for ‘lines’
rdplot: no visible global function definition for ‘lowess’
rdplot: no visible global function definition for ‘rgb’
simer: no visible global function definition for ‘runif’
simer: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  cor.test lines lowess rgb rnorm runif
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines")
  importFrom("stats", "cor.test", "lowess", "rnorm", "runif")
to your NAMESPACE file.
'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/HCmodelSets.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'diversitree', 'flexsurv'

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
Packages required but not available: 'glmnet', 'harmonicmeanp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'geometry', 'M3C', 'rgeos'

Packages suggested but not available for checking: 'alphahull', 'fields'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘klaR’
Package required but not available: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bigstatsr’

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/HDclassif.Rcheck/00install.out’ for details.
Package required but not available: ‘multtest’

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: ‘bit64’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘bit64’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'missForest', 'tidyverse'
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(hdImpute)
  > 
  > test_check("hdImpute")
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_feature_cor.R:1:1): (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_feature_cor.R:1:0
  ── Error (test_flatten_mat.R:1:1): (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_flatten_mat.R:1:0
  ── Error (test_hdImpute.R:1:1): (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_hdImpute.R:1:0
  ── Error (test_impute_batches.R:1:1): (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_impute_batches.R:1:0
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Getting-Started.Rmd’ using rmarkdown
Quitting from lines 47-49 (Getting-Started.Rmd) 
Error: processing vignette ‘Getting-Started.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
--- 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: 'scalreg', 'glmnet', 'linprog'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'NPCirc', 'Directional'

Package suggested but not available for checking: ‘mapproj’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
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/HDMD.Rcheck/00install.out’ for details.
Packages required but not available: 'glmnet', 'Rglpk'

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: 'glmnet', 'penalized', 'survAUC'

Package suggested but not available for checking: ‘doParallel’

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: ‘rtkore’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggjoy', 'ggpubr', 'Hmisc', 'questionr', 'MCMCpack', 'tidyverse'

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: 'rgdal', 'swfscMisc', 'rgeos'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'doParallel', 'expm', 'fastclime', 'clime'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘clime’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
coef.HDtweedie: no visible global function definition for ‘rbind2’
coef.cv.HDtweedie: no visible global function definition for ‘coef’
cv.tweediegrppath: no visible global function definition for ‘predict’
cv.tweediegrppath: no visible binding for global variable
  ‘weighted.mean’
cvcompute: no visible binding for global variable ‘weighted.mean’
error.bars: no visible global function definition for ‘segments’
lambda.interp: no visible global function definition for ‘approx’
plot.HDtweedie: no visible global function definition for ‘par’
plot.HDtweedie: no visible binding for global variable ‘plot.default’
plot.HDtweedie: no visible global function definition for ‘gray.colors’
plot.HDtweedie: no visible global function definition for ‘abline’
plot.cv.HDtweedie: no visible global function definition for ‘points’
plot.cv.HDtweedie: no visible global function definition for ‘axis’
plot.cv.HDtweedie: no visible global function definition for ‘abline’
predict.HDtweedie: no visible global function definition for ‘rbind2’
predict.HDtweedie: no visible global function definition for ‘cbind2’
predict.cv.HDtweedie: no visible global function definition for
  ‘predict’
Undefined global functions or variables:
  abline approx axis cbind2 coef gray.colors par plot.default points
  predict rbind2 segments weighted.mean
Consider adding
  importFrom("grDevices", "gray.colors")
  importFrom("graphics", "abline", "axis", "par", "plot.default",
             "points", "segments")
  importFrom("methods", "cbind2", "rbind2")
  importFrom("stats", "approx", "coef", "predict", "weighted.mean")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages required but not available: 'caret', 'glmnet', 'recipes'

Package suggested but not available for checking: ‘odbc’

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:
  'ggrepel', 'recipes', 'dials', 'tune', 'modeltime'

Packages suggested but not available for checking:
  'timetk', 'plotly', 'rsample'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'timetk', 'sqldf', 'ggrepel', 'plotly'

Package suggested but not available for checking: ‘uwot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'timetk', 'plotly', 'recipes', 'modeltime', 'workflowsets', 'earth'

Packages suggested but not available for checking:
  'rsample', 'healthyR', 'forecast', 'tidymodels', 'xts', 'TSA',
  'tune', 'dials'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'healthyR', 'healthyR.ts', 'healthyR.ai', 'TidyDensity'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Biobase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'plotly', 'viridis', 'dendextend', 'seriation', 'egg'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'doParallel', 'ggpubr'
Packages required but not available:
  'sampleSelection', 'PerformanceAnalytics'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/HEDA.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/hedgehog.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'BCEA', 'diagram', 'flexsurv', 'rgho'
Running examples in ‘heemod-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: apply_shift
> ### Title: Apply a time shift to a survival distribution
> ### Aliases: apply_shift
> 
> ### ** Examples
> 
> 
> dist1 <- define_survival(distribution = "gamma", rate = 0.25, shape = 3)
> shift_dist <- apply_shift(dist1, 4)
> compute_surv(dist1, 1:10)
Loading required namespace: flexsurv
Failed with error:  ‘there is no package called ‘flexsurv’’
Error in eval_surv.surv_dist(x, cycle_length * time_, ...) : 
  'flexsurv' package required.
Calls: compute_surv ... eval -> <Anonymous> -> eval_surv -> eval_surv.surv_dist
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘a_introduction.Rmd’ using rmarkdown
--- finished re-building ‘a_introduction.Rmd’

--- re-building ‘b_time_dependency.Rmd’ using rmarkdown
--- finished re-building ‘b_time_dependency.Rmd’

--- re-building ‘c_homogeneous.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'diagram''
Quitting from lines 75-76 (c_homogeneous.Rmd) 
Error: processing vignette ‘c_homogeneous.Rmd’ failed with diagnostics:
'diagram' package required for transition plot.
--- failed re-building ‘c_homogeneous.Rmd’

--- re-building ‘d_non_homogeneous.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'diagram''
Quitting from lines 162-163 (d_non_homogeneous.Rmd) 
Error: processing vignette ‘d_non_homogeneous.Rmd’ failed with diagnostics:
'diagram' package required for transition plot.
--- failed re-building ‘d_non_homogeneous.Rmd’

--- re-building ‘f_sensitivity.Rmd’ using rmarkdown
--- finished re-building ‘f_sensitivity.Rmd’

--- re-building ‘i_reproduction.Rmd’ using rmarkdown
--- finished re-building ‘i_reproduction.Rmd’

--- re-building ‘j_survival.Rmd’ using rmarkdown
--- finished re-building ‘j_survival.Rmd’

--- re-building ‘e_probabilistic.Rmd’ using rmarkdown_notangle
--- finished re-building ‘e_probabilistic.Rmd’

--- re-building ‘g_heterogeneity.Rmd’ using rmarkdown_notangle
--- finished re-building ‘g_heterogeneity.Rmd’

--- re-building ‘h_tabular.Rmd’ using rmarkdown_notangle
--- finished re-building ‘h_tabular.Rmd’

--- re-building ‘k_calibration.Rmd’ using rmarkdown_notangle

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 ‘k_calibration.Rmd’

SUMMARY: processing the following files failed:
  ‘c_homogeneous.Rmd’ ‘d_non_homogeneous.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘bit64’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sqldf’

Package suggested but not available for checking: ‘devtools’

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: ‘orthopolynom’

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/helloJavaWorld.Rcheck/00install.out’ for details.
Package required but not available: ‘taxize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lme4’

Packages suggested but not available for checking: 'fields', 'ppcor'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'graph', 'RBGL', 'doParallel'

Package suggested but not available for checking: ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

Packages suggested but not available for checking:
  'candisc', 'effects', 'mvinfluence'

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 suggested but not available for checking: ‘mapview’
Packages required but not available:
  'ergm', 'latentnet', 'mcgibbsit', 'sna', 'mlergm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘synbreed’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heritability.Rcheck/00install.out’ for details.
Packages required but not available:
  'cplm', 'DESeq2', 'lme4', 'SummarizedExperiment'

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: 'rgeos', 'fields'

Packages suggested but not available for checking:
  'autoimage', 'devtools', 'fda'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'flexsurv', 'msm'

Package suggested but not available for checking: ‘mstate’

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: ‘monomvn’
Package required but not available: ‘R2jags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hett.Rcheck/00install.out’ for details.
Packages required but not available: 'quantreg', 'doParallel', 'tidyverse'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking: 'devtools', 'glmnet'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'processmapR', 'DiagrammeR', 'petrinetR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'marray', 'affy', 'Biobase'
Packages required but not available: 'ggimage', 'showtext'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'seqinr', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dendextend’

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/hglm.data.Rcheck/00install.out’ for details.
Package required but not available: ‘hglm.data’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘genscore’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hgm.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
Package required but not available: ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘surveillance’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'latticeExtra', 'multcomp', 'vcd', 'Hmisc', 'Rmpfr'

Packages suggested but not available for checking:
  'car', 'Rcmdr', 'RcmdrPlugin.HH', 'microplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'cpr', 'magic'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'EMD', 'fields', 'spatstat.geom', 'spatstat.core', 'spatstat.linnet',
  '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/hibayes.Rcheck/00install.out’ for details.
Packages required but not available:
  'GenomicRanges', 'glmnet', 'rtracklayer', 'IRanges', 'GenomeInfoDb'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘devtools’
Packages required but not available: 'mc2d', 'rgeos', 'MCMCpack'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
‘:::’ call which should be ‘::’: ‘ggplot2:::guide_axis’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ‘:::’ calls:
  ‘ggplot2:::build_guides’ ‘ggplot2:::scales_list’
  See the note in ?`:::` about the use of this operator.
banded: no visible global function definition for ‘toeplitz’
gpband: no visible global function definition for ‘toeplitz’
hierband.cv: no visible global function definition for ‘cov’
hierband.cv: no visible binding for global variable ‘sd’
subdiag.thresh: no visible global function definition for ‘uniroot’
subdiag.thresh: no visible global function definition for ‘toeplitz’
Undefined global functions or variables:
  cov sd toeplitz uniroot
Consider adding
  importFrom("stats", "cov", "sd", "toeplitz", "uniroot")
to your NAMESPACE file.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'glmnet', 'hdi', 'SIHR'

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:
  'GGally', 'adegenet', 'diveRsity', 'entropart', 'mmod', 'hierfstat',
  'vegan', 'pegas'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'adegenet', 'gaston'

Package suggested but not available for checking: ‘pegas’

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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hierSDR.Rcheck/00install.out’ for details.
compute.contrasts: no visible binding for global variable ‘sd’
compute.contrasts: no visible global function definition for ‘cor’
compute.contrasts: no visible global function definition for ‘sd’
plot.hiertest: no visible global function definition for ‘legend’
Undefined global functions or variables:
  cor legend sd
Consider adding
  importFrom("graphics", "legend")
  importFrom("stats", "cor", "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/HIest.Rcheck/00install.out’ for details.
Packages required but not available: 'xts', 'quantmod'

Packages suggested but not available for checking: 'forecast', 'geojsonio'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fastclime’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RMallow’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'xts', 'quantmod'

Packages suggested but not available for checking: 'BMS', 'rugarch'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/highmean.Rcheck/00install.out’ for details.
Packages required but not available:
  'mlr3', 'mlr3proba', 'mlr3learners', 'coxme', 'missForest'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'fields', 'rgeos', 'spatstat', 'ks', 'spatstat.random',
  'spatstat.geom', 'spatstat.core'

Package suggested but not available for checking: ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/highSCREEN.Rcheck/00install.out’ for details.
Package required but not available: ‘gcdnet’

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: ‘bit64’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘haven’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggpubr', 'vegan', 'geiger', 'qgraph', 'FSA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
occupancy: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Packages required but not available: 'FD', 'geiger'

Package suggested but not available for checking: ‘betapart’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'raster', 'rayshader'

Package suggested but not available for checking: ‘rgdal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
data_simu: no visible global function definition for ‘runif’
data_simu: no visible global function definition for ‘rbinom’
data_simu: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rbinom rnorm runif
Consider adding
  importFrom("stats", "rbinom", "rnorm", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: ‘viridis’
Packages required but not available: 'glmnet', '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/hiPOD.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘readr’
'LazyData' is specified without a 'data' directory
Packages required but not available:
  'InterpretMSSpectrum', 'Rdisop', 'Biobase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'rms', 'ltm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'phytools', 'diversitree', 'paleotree', 'geiger', 'phangorn',
  'TreeSim', 'corHMM'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'car', 'heplots', 'effects', 'vcd'
Running examples in ‘HistData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CushnyPeebles
> ### Title: Cushny-Peebles Data: Soporific Effects of Scopolamine
> ###   Derivatives
> ### Aliases: CushnyPeebles CushnyPeeblesN
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(CushnyPeebles)
> # quick looks at the data
> plot(CushnyPeebles)
> boxplot(CushnyPeebles, ylab="Hours of Sleep", xlab="Treatment")
> 
> ##########################
> # Repeated measures MANOVA
> 
> CPmod <- lm(cbind(Control, L_hyoscyamine, L_hyoscine, DL_hyoscine) ~ 1, data=CushnyPeebles)
> 
> # Assign within-S factor and contrasts
> Treatment <- factor(colnames(CushnyPeebles), levels=colnames(CushnyPeebles))
> contrasts(Treatment) <- matrix(
+ 	c(-3, 1, 1, 1,
+ 	   0,-2, 1, 1,
+ 	   0, 0,-1, 1), ncol=3)
> colnames(contrasts(Treatment)) <- c("Control.Drug", "L.DL", "L_hy.DL_hy")
> 
> Treats <- data.frame(Treatment)
> if (require(car)) {
+ (CPaov <- Anova(CPmod, idata=Treats, idesign= ~Treatment))
+ }
Loading required package: car
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘car’
> summary(CPaov, univariate=FALSE)
Error in summary(CPaov, univariate = FALSE) : object 'CPaov' not found
Execution halted
Package required but not available: ‘FactoMineR’

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: 'roprov', 'CodeDepends'

Package suggested but not available for checking: ‘trackr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'glmnet', 'speedglm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘HadoopStreaming’
Packages suggested but not available for checking: 'sna', 'bipartite'
Running examples in ‘HiveR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: adj2HPD
> ### Title: Process an Adjacency Graph into a HivePlotData Object
> ### Aliases: adj2HPD
> ### Keywords: utilities
> 
> ### ** Examples
> 
> 
> ### Example 1: a bipartite network
> ### Note: this first example has questionable scientific value!
> ### The purpose is to show how to troubleshoot and
> ### manipulate a HivePlotData object.
> 
> require(bipartite)
Loading required package: bipartite
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘bipartite’
> data(Safariland) # This is a bipartite network
Warning in data(Safariland) : data set ‘Safariland’ not found
> 
> # You may wish to do ?Safariland or ?Safari for background
> 
> hive1 <- adj2HPD(Safariland, desc = "Safariland data set from bipartite")
Error in adj2HPD(Safariland, desc = "Safariland data set from bipartite") : 
  object 'Safariland' not found
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘HiveR.Rmd’ using rmarkdown
Quitting from lines 24-41 (HiveR.Rmd) 
Error: processing vignette ‘HiveR.Rmd’ failed with diagnostics:
there is no package called 'sna'
--- failed re-building ‘HiveR.Rmd’

SUMMARY: processing the following file failed:
  ‘HiveR.Rmd’

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
Package required but not available: ‘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/hkevp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hkex.api.Rcheck/00install.out’ for details.
Package required but not available: ‘MCMCpack’

Package suggested but not available for checking: ‘FGN’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'devtools', 'tidyverse', 'readr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggrepel’

Packages suggested but not available for checking:
  'mlmRev', 'lme4', 'car', 'qqplotr'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'lme4', 'mlmRev', 'MCMCpack'
Running ‘testthat.R’ [24s/38s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(hmclearn)
  > 
  > test_check("hmclearn")
  Summary of MCMC simulation
  
  Summary of MCMC simulation
  
  Summary of MCMC simulation
  
  Summary of MCMC simulation
  
  Summary of MCMC simulation
  
  Summary of MCMC simulation
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 21 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_paper.R:90:3): paper examples ───────────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `library(lme4)`: there is no package called 'lme4'
  Backtrace:
      ▆
   1. └─base::library(lme4) at test_paper.R:90:2
  ── Error (test_vignettes.R:113:3): vignette examples ───────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'mlmRev'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test_vignettes.R:113:2
   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 21 ]
  Error: Test failures
  Execution halted
Packages required but not available: 'viridis', 'GGally'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'broom.mixed', 'lme4', 'MCMCglmm', 'msm', 'tmvtnorm'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'latticeExtra', 'viridis'

Packages suggested but not available for checking: 'rms', 'plotly'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
baumwelchcont: no visible global function definition for ‘dnorm’
hmmcontSimul: no visible global function definition for ‘rnorm’
hmmcontSimul: no visible global function definition for ‘rbinom’
plot.ContObservHMM: no visible global function definition for ‘lines’
statesDistributionsPlot: no visible global function definition for
  ‘dnorm’
statesDistributionsPlot: no visible global function definition for ‘sd’
statesDistributionsPlot: no visible global function definition for
  ‘lines’
statesDistributionsPlot: no visible global function definition for
  ‘legend’
summary.ContObservHMM: no visible global function definition for ‘sd’
Undefined global functions or variables:
  dnorm legend lines rbinom rnorm sd
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "dnorm", "rbinom", "rnorm", "sd")
to your NAMESPACE file.
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 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: ‘depmixS4’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doParallel', 'vegan', 'rpart.plot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'HMP', 'doParallel'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'fields', 'MCMCpack'

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/HMVD.Rcheck/00install.out’ for details.
Packages required but not available: 'NMF', 'rasterImage'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'lme4', 'gamlss', 'gamlss.dist', 'aods3', 'glmmADMB', 'latticeExtra'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hnp.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘csampling’
Packages required but not available:
  'bamsignals', 'Biostrings', 'GenomicRanges',
  'GenomicTools.fileHandler', 'IRanges', 'R.utils', 'Rsamtools',
  'S4Vectors', 'seqinr'

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: ‘MplusAutomation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'readr', 'R.utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘furrr’

Packages suggested but not available for checking: 'ggrepel', 'RSQLite'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘survey’

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: 'orthopolynom', 'quantmod'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
hornpa: no visible global function definition for ‘rnorm’
hornpa: no visible global function definition for ‘cor’
hornpa: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  cor quantile rnorm
Consider adding
  importFrom("stats", "cor", "quantile", "rnorm")
to your NAMESPACE file.
Package required but not available: ‘msm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Hmisc’
Running examples in ‘horseshoe-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HS.normal.means
> ### Title: The horseshoe prior for the sparse normal means problem
> ### Aliases: HS.normal.means
> 
> ### ** Examples
> 
> #Empirical Bayes example with 20 signals, rest is noise
> #Posterior mean for the signals is plotted
> #And variable selection is performed using the credible intervals
> #And the credible intervals are plotted
> truth <- c(rep(0, 80), rep(8, 20))
> data <-  truth + rnorm(100, 1)
> tau.hat <- HS.MMLE(data, Sigma2 = 1)
> res.HS1 <- HS.normal.means(data, method.tau = "fixed", tau = tau.hat,
+ method.sigma = "fixed", Sigma2 = 1)
[1] 1000
[1] 2000
[1] 3000
[1] 4000
[1] 5000
[1] 6000
> #Plot the posterior mean against the data (signals in blue)
> plot(data, res.HS1$BetaHat, col = c(rep("black", 80), rep("blue", 20)))
> #Find the selected betas (ideally, the last 20 are equal to 1)
> HS.var.select(res.HS1, data, method = "intervals")
  [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 [38] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0
 [75] 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
> #Plot the credible intervals
> library(Hmisc)
Error in library(Hmisc) : there is no package called ‘Hmisc’
Execution halted
checkRd: (7) simHostSwitch.Rd:63: \item in \describe must have non-empty label
checkRd: (7) simHostSwitch.Rd:64: \item in \describe must have non-empty label
checkRd: (7) simHostSwitch.Rd:76: \item in \describe must have non-empty label
checkRd: (7) simHostSwitch.Rd:77: \item in \describe must have non-empty label
checkRd: (7) simHostSwitch.Rd:78: \item in \describe must have non-empty label
checkRd: (7) simHostSwitch.Rd:79: \item in \describe must have non-empty label
checkRd: (7) simHostSwitch.Rd:80: \item in \describe must have non-empty label
checkRd: (7) simHostSwitch.Rd:81: \item in \describe must have non-empty label
Package suggested but not available for checking: ‘miceadds’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Using_Hot_Deck_Data.Rmd’ using rmarkdown
Quitting from lines 97-101 (Using_Hot_Deck_Data.Rmd) 
Error: processing vignette ‘Using_Hot_Deck_Data.Rmd’ failed with diagnostics:
there is no package called 'miceadds'
--- failed re-building ‘Using_Hot_Deck_Data.Rmd’

SUMMARY: processing the following file failed:
  ‘Using_Hot_Deck_Data.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'FactoMineR', 'ggforce'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Hotelling.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hotspots.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘jomo’
Running ‘testthat.R’ [3s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(howManyImputations)
  > 
  > test_check("howManyImputations")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 8 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-how_many_imputations.R:31:3): jomo ──────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `library(jomo)`: there is no package called 'jomo'
  Backtrace:
      ▆
   1. └─base::library(jomo) at test-how_many_imputations.R:31:2
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 8 ]
  Error: Test failures
  Execution halted
Packages suggested but not available for checking: 'sampleSelection', 'GA'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/HPbayes.Rcheck/00install.out’ for details.
Packages required but not available: 'imputeTS', 'forecast', 'pdp'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'fields', 'distrEx'
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/HPLB.Rcheck/00install.out’ for details.
Package required but not available: ‘Rgraphviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
bracket: no visible global function definition for ‘segments’
Undefined global functions or variables:
  segments
Consider adding
  importFrom("graphics", "segments")
to your NAMESPACE file.
Package suggested but not available for checking: ‘RISCA’
Packages required but not available: 'doBy', 'pseudorank'

Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘fields’
Packages suggested but not available for checking:
  'coin', 'flexmix', 'lme4', 'party', 'vcd', 'multcomp', 'mboost',
  'partykit', 'wordcloud', 'TH.data'
Running examples in ‘HSAUR2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BCG
> ### Title: BCG Vaccine Data
> ### Aliases: BCG
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
>   data("BCG", package = "HSAUR2")
> 
>   ### sort studies w.r.t. sample size
>   BCG <- BCG[order(rowSums(BCG[,2:5])),]
> 
>   ### to long format
>   BCGlong <- with(BCG, data.frame(Freq = c(BCGTB, BCGVacc - BCGTB, 
+                                            NoVaccTB, NoVacc - NoVaccTB),
+                   infected = rep(rep(factor(c("yes", "no")), 
+                                  rep(nrow(BCG), 2)), 2),
+                   vaccined = rep(factor(c("yes", "no")), 
+                                  rep(nrow(BCG) * 2, 2)),
+                   study = rep(factor(Study, levels = as.character(Study)), 
+                               4)))
> 
>   ### doubledecker plot
>   library("vcd")
Error in library("vcd") : there is no package called ‘vcd’
Execution halted
Packages suggested but not available for checking:
  'coin', 'flexmix', 'lme4', 'maptools', 'mboost', 'multcomp',
  'partykit', 'quantreg', 'TH.data', 'vcd', 'wordcloud'
Running examples in ‘HSAUR3-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BCG
> ### Title: BCG Vaccine Data
> ### Aliases: BCG
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
>   data("BCG", package = "HSAUR3")
> 
>   ### sort studies w.r.t. sample size
>   BCG <- BCG[order(rowSums(BCG[,2:5])),]
> 
>   ### to long format
>   BCGlong <- with(BCG, data.frame(Freq = c(BCGTB, BCGVacc - BCGTB, 
+                                            NoVaccTB, NoVacc - NoVaccTB),
+                   infected = rep(rep(factor(c("yes", "no")), 
+                                  rep(nrow(BCG), 2)), 2),
+                   vaccined = rep(factor(c("yes", "no")), 
+                                  rep(nrow(BCG) * 2, 2)),
+                   study = rep(factor(Study, levels = as.character(Study)), 
+                               4)))
> 
>   ### doubledecker plot
>   library("vcd")
Error in library("vcd") : there is no package called ‘vcd’
Execution halted
Packages suggested but not available for checking:
  'coin', 'flexmix', 'lme4', 'party', 'vcd', 'TH.data'
Packages required but not available: 'raster', 'rgdal', 'caret'

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: ‘raster’
Error(s) in re-building vignettes:
  ...
--- re-building ‘hSDM.Rmd’ using rmarkdown
Quitting from lines 60-64 (hSDM.Rmd) 
Error: processing vignette ‘hSDM.Rmd’ failed with diagnostics:
there is no package called 'raster'
--- failed re-building ‘hSDM.Rmd’

--- re-building ‘publications.Rmd’ using rmarkdown
--- finished re-building ‘publications.Rmd’

SUMMARY: processing the following file failed:
  ‘hSDM.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hsem.Rcheck/00install.out’ for details.
hsicCCA: no visible global function definition for ‘median’
hsicCCA: no visible global function definition for ‘dist’
hsicCCAfunc: no visible global function definition for ‘rnorm’
hsicCCAfunc: no visible global function definition for ‘runif’
hsicCCAfunc: no visible global function definition for ‘optim’
ktaCCA: no visible global function definition for ‘median’
ktaCCA: no visible global function definition for ‘dist’
ktaCCAfunc: no visible global function definition for ‘rnorm’
ktaCCAfunc: no visible global function definition for ‘runif’
ktaCCAfunc: no visible global function definition for ‘optim’
Undefined global functions or variables:
  dist median optim rnorm runif
Consider adding
  importFrom("stats", "dist", "median", "optim", "rnorm", "runif")
to your NAMESPACE file.
Rd file 'hsicCCA.Rd':
  \usage lines wider than 90 characters:
     hsicCCA(x, y, M, sigmax = NULL, sigmay = NULL, numrepeat = 5, numiter = 100, reltolstop = 1e-04)

Rd file 'ktaCCA.Rd':
  \usage lines wider than 90 characters:
     ktaCCA(x, y, M, sigmax = NULL, sigmay = NULL, numrepeat = 5, numiter = 100, reltolstop = 1e-04)

These lines will be truncated in the PDF manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hsmm.Rcheck/00install.out’ for details.
Package required but not available: ‘snowfall’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘npregfast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘hsphase’

Packages suggested but not available for checking:
  'AlphaSimR', 'doParallel'

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
Packages required but not available: 'BCBCSF', '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
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: ‘Hmisc’
Running ‘testInteractive.R’ [1s/2s]
  Running ‘testthat.R’ [11s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check('htmlTable')
  Loading required package: htmlTable
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 487 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-tidyHtmlTable_Hmisc_latex.R:85:3): Works with Hmisc::latex ──────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'Hmisc'
  Backtrace:
       ▆
    1. ├─testthat::expect_output(...) at test-tidyHtmlTable_Hmisc_latex.R:85:2
    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. ├─... %>% ...
   11. ├─htmlTable::tidyHtmlTable(...)
   12. ├─htmlTable:::tidyHtmlTable.data.frame(...)
   13. │ └─base::do.call(table_fn, htmlTable_args)
   14. └─base::loadNamespace(x)
   15.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   16.     └─base withOneRestart(expr, restarts[[1L]])
   17.       └─base doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 487 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘complex_tables.Rmd’ using rmarkdown
Quitting from lines 120-160 (complex_tables.Rmd) 
Error: processing vignette ‘complex_tables.Rmd’ failed with diagnostics:
there is no package called 'Hmisc'
--- failed re-building ‘complex_tables.Rmd’

--- re-building ‘general.Rmd’ using rmarkdown
--- finished re-building ‘general.Rmd’

--- re-building ‘text_formatters.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following object is masked from 'package:reshape':

    rename

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 ‘text_formatters.Rmd’

--- re-building ‘tidyHtmlTable.Rmd’ using rmarkdown

Attaching package: 'tidyr'

The following objects are masked from 'package:reshape':

    expand, smiths

The following object is masked from 'package:magrittr':

    extract

Warning in removeRowsWithNA(., skip_removal_warning = skip_removal_warning) :
  NA values were detected in the following columns of the tidy dataset: value. 6 row(s) in the tidy dataset were removed.
Warning in removeRowsWithNA(., skip_removal_warning = skip_removal_warning) :
  NA values were detected in the following columns of the tidy dataset: value. 6 row(s) in the tidy dataset were removed.
--- finished re-building ‘tidyHtmlTable.Rmd’

SUMMARY: processing the following file failed:
  ‘complex_tables.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/HTMLUtils.Rcheck/00install.out’ for details.
Packages required but not available: 'edgeR', 'capushe'

Packages suggested but not available for checking: 'HTSFilter', 'Biobase'

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:
  'readr', 'RSQLite', 'openair', 'raster', 'editData'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'vegan', 'DESeq2', 'phyloseq'

Package suggested but not available for checking: ‘doParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'msm', 'survey'

Packages suggested but not available for checking:
  'R.rsp', 'GGally', 'ks', 'viridis', 'ggrepel'

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: ‘httptest’
Running ‘spelling.R’ [0s/1s]
  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 ‘httpcache.Rmd’ using rmarkdown
Quitting from lines 91-92 (httpcache.Rmd) 
Error: processing vignette ‘httpcache.Rmd’ failed with diagnostics:
there is no package called 'httptest'
--- failed re-building ‘httpcache.Rmd’

SUMMARY: processing the following file failed:
  ‘httpcache.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/httping.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/httptest.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘jose’
Running examples in ‘httr2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: jwt_claim
> ### Title: Create and encode a JWT
> ### Aliases: jwt_claim jwt_encode_sig jwt_encode_hmac
> 
> ### ** Examples
> 
> claim <- jwt_claim()
Error in loadNamespace(x) : there is no package called ‘jose’
Calls: jwt_claim ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Package suggested but not available for checking: ‘readr’
'LazyData' is specified without a 'data' directory
Packages required but not available: 'showtext', 'qrcode'

Package suggested but not available for checking: ‘inti’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/humanFormat.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/HUM.Rcheck/00install.out’ for details.
Packages required but not available: 'rstan', 'Hmisc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Packages required but not available: 'ggmap', 'mapproj'

Package suggested but not available for checking: ‘hurricaneexposuredata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'Hmisc', 'readr', 'survey'
Packages suggested but not available for checking:
  'AER', 'broom.mixed', 'devtools', 'lme4', 'lmtest'
Error(s) in re-building vignettes:
  ...
--- re-building ‘design-principles.Rmd’ using rmarkdown
--- finished re-building ‘design-principles.Rmd’

--- re-building ‘huxreg.Rmd’ using rmarkdown
Quitting from lines 231-235 (huxreg.Rmd) 
Error: processing vignette ‘huxreg.Rmd’ failed with diagnostics:
there is no package called 'lmtest'
--- failed re-building ‘huxreg.Rmd’

--- re-building ‘huxtable.Rmd’ using rmarkdown
--- finished re-building ‘huxtable.Rmd’

--- re-building ‘themes.Rhtml’ using knitr
--- finished re-building ‘themes.Rhtml’

SUMMARY: processing the following file failed:
  ‘huxreg.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘MCMCpack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'doFuture', 'doRNG'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘spatsoc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
HW.plain: 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: ‘raster’

Package suggested but not available for checking: ‘rgdal’

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: 'ada', 'Rmalschains', 'glmnet'

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: 'DiagrammeR', 'graph', '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/hydroApps.Rcheck/00install.out’ for details.
Packages required but not available: 'hydroTSM', 'xts'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'Hmisc', 'hydroTSM', 'hydroGOF', 'vioplot'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggpmisc’

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.
checkRd: (7) baseflows.Rd:44: \item in \value must have non-empty label
checkRd: (7) baseflows.Rd:47: \item in \value must have non-empty label